From c60bf4be2a9a7d7b1597592f655dcfe97a00cefa Mon Sep 17 00:00:00 2001
From: Daniel Incicau <daniel_incicau@yahoo.com>
Date: Fri, 15 Mar 2024 12:43:40 +0100
Subject: [PATCH 1/4] Some attempt to link inputs

---
 .idea/.gitignore                              |    8 +
 .idea/inspectionProfiles/Project_Default.xml  |   31 +
 .../inspectionProfiles/profiles_settings.xml  |    6 +
 .idea/misc.xml                                |    7 +
 .idea/modules.xml                             |    8 +
 .idea/omni_workflow.iml                       |    8 +
 .idea/snakemake-settings.xml                  |    4 +
 .idea/vcs.xml                                 |    6 +
 .../2024-03-11T144829.779841.snakemake.log    |  130 ++
 .../2024-03-12T151017.402548.snakemake.log    |  113 ++
 .../2024-03-12T152038.551300.snakemake.log    |    2 +
 .../2024-03-12T182448.069386.snakemake.log    |   10 +
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 .../2024-03-14T150910.862226.snakemake.log    |  255 +++
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 .../2024-03-14T153156.720661.snakemake.log    |    7 +
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 .../2024-03-14T154013.525590.snakemake.log    |  196 +++
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 .../2024-03-14T160916.155879.snakemake.log    |  267 +++
 .../2024-03-14T161002.065257.snakemake.log    |   86 +
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 .../2024-03-14T162346.370984.snakemake.log    |    3 +
 .../2024-03-14T162407.717451.snakemake.log    |    3 +
 .../2024-03-14T162433.205078.snakemake.log    |  267 +++
 .../2024-03-14T162707.977496.snakemake.log    |    2 +
 .../2024-03-14T162714.901875.snakemake.log    |  267 +++
 .../2024-03-14T162753.336457.snakemake.log    |  267 +++
 .../2024-03-14T163013.516825.snakemake.log    |    9 +
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 .../2024-03-14T163101.934544.snakemake.log    |   11 +
 .../2024-03-14T163138.439586.snakemake.log    |  267 +++
 .../2024-03-14T163231.507025.snakemake.log    |   11 +
 .../2024-03-14T163257.053515.snakemake.log    |    9 +
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 Pipfile                                       |    5 +-
 Pipfile.lock                                  | 1474 +++++++++++++++++
 Snakefile                                     |   13 +-
 log/system_profiling.txt                      |   12 +
 main.py                                       |    9 +-
 out/data/D1/default/D1.meta.json              |    7 +
 out/data/D1/default/D1.txt.gz                 |    7 +
 out/data/D1/default/D1_params.txt             |    7 +
 .../D1/default/process/P1/default/D1.txt.gz   |    7 +
 .../methods/M1/default/D1.model.out.gz        |    7 +
 .../methods/M2/default/D1.model.out.gz        |    7 +
 .../D1/default/process/P2/default/D1.txt.gz   |    7 +
 .../methods/M1/default/D1.model.out.gz        |    7 +
 .../methods/M2/default/D1.model.out.gz        |    7 +
 out/data/D2/default/D2.meta.json              |    7 +
 out/data/D2/default/D2.txt.gz                 |    7 +
 out/data/D2/default/D2_params.txt             |    7 +
 .../D2/default/process/P1/default/D2.txt.gz   |    7 +
 .../methods/M1/default/D2.model.out.gz        |    7 +
 .../methods/M2/default/D2.model.out.gz        |    7 +
 .../D2/default/process/P2/default/D2.txt.gz   |    7 +
 .../methods/M1/default/D2.model.out.gz        |    7 +
 .../methods/M2/default/D2.model.out.gz        |    7 +
 output_dag.png                                |  Bin 0 -> 117960 bytes
 snakemake.py                                  |    8 +-
 src/__pycache__/dag.cpython-311.pyc           |  Bin 0 -> 7595 bytes
 src/__pycache__/formatter.cpython-311.pyc     |  Bin 0 -> 2051 bytes
 src/__pycache__/helpers.cpython-311.pyc       |  Bin 0 -> 2163 bytes
 .../__pycache__/__init__.cpython-311.pyc      |  Bin 0 -> 259 bytes
 .../__pycache__/converter.cpython-311.pyc     |  Bin 0 -> 3653 bytes
 .../model_converter.cpython-311.pyc           |  Bin 0 -> 6761 bytes
 .../yaml_converter.cpython-311.pyc            |  Bin 0 -> 11521 bytes
 src/converter/model_converter.py              |   19 +-
 src/converter/yaml_converter.py               |    3 +
 src/dag.py                                    |    2 +-
 src/formatter.py                              |   34 +-
 247 files changed, 8997 insertions(+), 26 deletions(-)
 create mode 100644 .idea/.gitignore
 create mode 100644 .idea/inspectionProfiles/Project_Default.xml
 create mode 100644 .idea/inspectionProfiles/profiles_settings.xml
 create mode 100644 .idea/misc.xml
 create mode 100644 .idea/modules.xml
 create mode 100644 .idea/omni_workflow.iml
 create mode 100644 .idea/snakemake-settings.xml
 create mode 100644 .idea/vcs.xml
 create mode 100644 .snakemake/log/2024-03-11T144829.779841.snakemake.log
 create mode 100644 .snakemake/log/2024-03-12T151017.402548.snakemake.log
 create mode 100644 .snakemake/log/2024-03-12T152038.551300.snakemake.log
 create mode 100644 .snakemake/log/2024-03-12T182448.069386.snakemake.log
 create mode 100644 .snakemake/log/2024-03-12T182552.532249.snakemake.log
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 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AxLy1hXzFfXy1iXzBfMS9tZXRob2RzL00xL2RlZmF1bHQvRDIubW9kZWwub3V0Lmd6
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 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AxLy1hXzFfXy1iXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMi9EMi5tb2RlbC5vdXQuZ3o=
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvRDEudHh0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvRDIudHh0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvbWV0aG9kcy9NMS9kZWZhdWx0L0QxLm1vZGVsLm91dC5neg==
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvbWV0aG9kcy9NMS9kZWZhdWx0L0QyLm1vZGVsLm91dC5neg==
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvbWV0aG9kcy9NMi9kZWZhdWx0L0QxLm1vZGVsLm91dC5neg==
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyL2RlZmF1bHQvbWV0aG9kcy9NMi9kZWZhdWx0L0QyLm1vZGVsLm91dC5neg==
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzBfXy1jXzAvRDIudHh0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzBfXy1jXzAvbWV0aG9kcy9NMS9kZWZhdWx0L0QyLm1vZGVsLm91dC5neg==
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzBfXy1jXzAvbWV0aG9kcy9NMi8tZDFfXy1lXzEvRDIubW9kZWwub3V0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzBfXy1jXzAvbWV0aG9kcy9NMi8tZDFfXy1lXzIvRDIubW9kZWwub3V0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9EMi50eHQuZ3o=
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00xL2RlZmF1bHQvRDIubW9kZWwub3V0Lmd6
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMS9EMi5tb2RlbC5vdXQuZ3o=
 create mode 100644 .snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMi9EMi5tb2RlbC5vdXQuZ3o=
 create mode 100644 .snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMS50eHQ=
 create mode 100644 .snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMi50eHQ=
 create mode 100644 .snakemake/metadata/bG9nL3N5c3RlbV9wcm9maWxpbmcudHh0
 create mode 100644 Pipfile.lock
 create mode 100644 log/system_profiling.txt
 create mode 100644 out/data/D1/default/D1.meta.json
 create mode 100644 out/data/D1/default/D1.txt.gz
 create mode 100644 out/data/D1/default/D1_params.txt
 create mode 100644 out/data/D1/default/process/P1/default/D1.txt.gz
 create mode 100644 out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
 create mode 100644 out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
 create mode 100644 out/data/D1/default/process/P2/default/D1.txt.gz
 create mode 100644 out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
 create mode 100644 out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
 create mode 100644 out/data/D2/default/D2.meta.json
 create mode 100644 out/data/D2/default/D2.txt.gz
 create mode 100644 out/data/D2/default/D2_params.txt
 create mode 100644 out/data/D2/default/process/P1/default/D2.txt.gz
 create mode 100644 out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
 create mode 100644 out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
 create mode 100644 out/data/D2/default/process/P2/default/D2.txt.gz
 create mode 100644 out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
 create mode 100644 out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
 create mode 100644 output_dag.png
 create mode 100644 src/__pycache__/dag.cpython-311.pyc
 create mode 100644 src/__pycache__/formatter.cpython-311.pyc
 create mode 100644 src/__pycache__/helpers.cpython-311.pyc
 create mode 100644 src/converter/__pycache__/__init__.cpython-311.pyc
 create mode 100644 src/converter/__pycache__/converter.cpython-311.pyc
 create mode 100644 src/converter/__pycache__/model_converter.cpython-311.pyc
 create mode 100644 src/converter/__pycache__/yaml_converter.cpython-311.pyc

diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000..13566b8
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,8 @@
+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 0000000..fa417cc
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,31 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="18">
+            <item index="0" class="java.lang.String" itemvalue="pandas" />
+            <item index="1" class="java.lang.String" itemvalue="scipy" />
+            <item index="2" class="java.lang.String" itemvalue="seaborn" />
+            <item index="3" class="java.lang.String" itemvalue="scikit_learn" />
+            <item index="4" class="java.lang.String" itemvalue="matplotlib" />
+            <item index="5" class="java.lang.String" itemvalue="torch" />
+            <item index="6" class="java.lang.String" itemvalue="numpy" />
+            <item index="7" class="java.lang.String" itemvalue="torchvision" />
+            <item index="8" class="java.lang.String" itemvalue="opencv_python" />
+            <item index="9" class="java.lang.String" itemvalue="Pillow" />
+            <item index="10" class="java.lang.String" itemvalue="scikit-image" />
+            <item index="11" class="java.lang.String" itemvalue="louvain" />
+            <item index="12" class="java.lang.String" itemvalue="python-louvain" />
+            <item index="13" class="java.lang.String" itemvalue="anndata" />
+            <item index="14" class="java.lang.String" itemvalue="scikit-learn" />
+            <item index="15" class="java.lang.String" itemvalue="scanpy" />
+            <item index="16" class="java.lang.String" itemvalue="igraph" />
+            <item index="17" class="java.lang.String" itemvalue="papermill" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+  </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000..105ce2d
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000..630cda0
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="Pipenv (omni_workflow)" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Pipenv (omni_workflow)" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000..6bcf8f9
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/omni_workflow.iml" filepath="$PROJECT_DIR$/.idea/omni_workflow.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/omni_workflow.iml b/.idea/omni_workflow.iml
new file mode 100644
index 0000000..88ab266
--- /dev/null
+++ b/.idea/omni_workflow.iml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Pipenv (omni_workflow)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/.idea/snakemake-settings.xml b/.idea/snakemake-settings.xml
new file mode 100644
index 0000000..cea4ebc
--- /dev/null
+++ b/.idea/snakemake-settings.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="SmkProjectSettings" sdk="Pipenv (omni_workflow)" enabled="true" />
+</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..35eb1dd
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/.snakemake/log/2024-03-11T144829.779841.snakemake.log b/.snakemake/log/2024-03-11T144829.779841.snakemake.log
new file mode 100644
index 0000000..101faf2
--- /dev/null
+++ b/.snakemake/log/2024-03-11T144829.779841.snakemake.log
@@ -0,0 +1,130 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                   count
+------------------  -------
+D1                        1
+D2                        1
+all                       1
+start_benchmark           1
+wildcard_awareness        2
+total                     6
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 3
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Mon Mar 11 14:48:29 2024]
+Finished job 3.
+1 of 6 steps (17%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule D1:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 2
+    reason: Missing output files: data/D1/default/D1.meta.json, data/D1/default/D1.txt.gz, data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+            echo no wildcards here Im afraid! > data/D1/default/D1.txt.gz
+            echo  > data/D1/default/D1.meta.json
+            echo  > data/D1/default/D1_params.txt
+            
+[Mon Mar 11 14:48:29 2024]
+Finished job 2.
+2 of 6 steps (33%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule D2:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 4
+    reason: Missing output files: data/D2/default/D2.meta.json, data/D2/default/D2_params.txt, data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+            echo no wildcards here Im afraid! > data/D2/default/D2.txt.gz
+            echo  > data/D2/default/D2.meta.json
+            echo  > data/D2/default/D2_params.txt
+            
+[Mon Mar 11 14:48:29 2024]
+Finished job 4.
+3 of 6 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule wildcard_awareness:
+    input: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt, data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    output: log/data_default_D1.txt
+    jobid: 1
+    reason: Missing output files: log/data_default_D1.txt; Input files updated by another job: data/D2/default/D2.meta.json, data/D1/default/D1.txt.gz, data/D2/default/D2.txt.gz, data/D1/default/D1.meta.json, data/D2/default/D2_params.txt, data/D1/default/D1_params.txt
+    wildcards: stage=data, params=default, id=D1
+    resources: tmpdir=/tmp
+
+
+        echo id=D1,params=default,stage=data > log/data_default_D1.txt
+        
+[Mon Mar 11 14:48:29 2024]
+Finished job 1.
+4 of 6 steps (67%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule wildcard_awareness:
+    input: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt, data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    output: log/data_default_D2.txt
+    jobid: 5
+    reason: Missing output files: log/data_default_D2.txt; Input files updated by another job: data/D2/default/D2.meta.json, data/D1/default/D1.txt.gz, data/D2/default/D2.txt.gz, data/D1/default/D1.meta.json, data/D2/default/D2_params.txt, data/D1/default/D1_params.txt
+    wildcards: stage=data, params=default, id=D2
+    resources: tmpdir=/tmp
+
+
+        echo id=D2,params=default,stage=data > log/data_default_D2.txt
+        
+[Mon Mar 11 14:48:29 2024]
+Finished job 5.
+5 of 6 steps (83%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Mon Mar 11 14:48:29 2024]
+localrule all:
+    input: log/data_default_D1.txt, log/data_default_D2.txt
+    jobid: 0
+    reason: Input files updated by another job: log/data_default_D1.txt, log/data_default_D2.txt
+    resources: tmpdir=/tmp
+
+[Mon Mar 11 14:48:29 2024]
+Finished job 0.
+6 of 6 steps (100%) done
+Complete log: .snakemake/log/2024-03-11T144829.779841.snakemake.log
diff --git a/.snakemake/log/2024-03-12T151017.402548.snakemake.log b/.snakemake/log/2024-03-12T151017.402548.snakemake.log
new file mode 100644
index 0000000..468fc00
--- /dev/null
+++ b/.snakemake/log/2024-03-12T151017.402548.snakemake.log
@@ -0,0 +1,113 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                    count
+-------------------  -------
+M1_run_module              2
+M2_run_module              2
+all                        1
+materialize_dataset        2
+total                      7
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Code has changed since last execution
+    wildcards: dataset=D1, params=default
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 1.
+1 of 7 steps (14%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Code has changed since last execution
+    wildcards: dataset=D2, params=default
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 3.
+2 of 7 steps (29%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 6.
+3 of 7 steps (43%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 5.
+4 of 7 steps (57%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 4.
+5 of 7 steps (71%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 7.
+6 of 7 steps (86%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Tue Mar 12 15:10:17 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, data/D1/default/D1_params.txt
+    resources: tmpdir=/tmp
+
+[Tue Mar 12 15:10:17 2024]
+Finished job 0.
+7 of 7 steps (100%) done
+Complete log: .snakemake/log/2024-03-12T151017.402548.snakemake.log
diff --git a/.snakemake/log/2024-03-12T152038.551300.snakemake.log b/.snakemake/log/2024-03-12T152038.551300.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-12T152038.551300.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-12T182448.069386.snakemake.log b/.snakemake/log/2024-03-12T182448.069386.snakemake.log
new file mode 100644
index 0000000..4d7c5ed
--- /dev/null
+++ b/.snakemake/log/2024-03-12T182448.069386.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+        data/D2/default/D2_params.txt
+        data/D1/default/D1_params.txt
diff --git a/.snakemake/log/2024-03-12T182552.532249.snakemake.log b/.snakemake/log/2024-03-12T182552.532249.snakemake.log
new file mode 100644
index 0000000..d76aec7
--- /dev/null
+++ b/.snakemake/log/2024-03-12T182552.532249.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        data/D2/default/D2_params.txt
+        out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+        data/D1/default/D1_params.txt
+        out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
diff --git a/.snakemake/log/2024-03-12T182558.810392.snakemake.log b/.snakemake/log/2024-03-12T182558.810392.snakemake.log
new file mode 100644
index 0000000..ebe8827
--- /dev/null
+++ b/.snakemake/log/2024-03-12T182558.810392.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        data/D1/default/D1_params.txt
+        out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+        data/D2/default/D2_params.txt
+        out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
diff --git a/.snakemake/log/2024-03-12T182735.903095.snakemake.log b/.snakemake/log/2024-03-12T182735.903095.snakemake.log
new file mode 100644
index 0000000..1d76631
--- /dev/null
+++ b/.snakemake/log/2024-03-12T182735.903095.snakemake.log
@@ -0,0 +1,6 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        data/D1/default/D1_params.txt
+        data/D2/default/D2_params.txt
diff --git a/.snakemake/log/2024-03-12T182756.402754.snakemake.log b/.snakemake/log/2024-03-12T182756.402754.snakemake.log
new file mode 100644
index 0000000..0c35687
--- /dev/null
+++ b/.snakemake/log/2024-03-12T182756.402754.snakemake.log
@@ -0,0 +1,6 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        data/D2/default/D2_params.txt
+        data/D1/default/D1_params.txt
diff --git a/.snakemake/log/2024-03-13T102855.125725.snakemake.log b/.snakemake/log/2024-03-13T102855.125725.snakemake.log
new file mode 100644
index 0000000..0c35687
--- /dev/null
+++ b/.snakemake/log/2024-03-13T102855.125725.snakemake.log
@@ -0,0 +1,6 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 41:
+Missing input files for rule all:
+    affected files:
+        data/D2/default/D2_params.txt
+        data/D1/default/D1_params.txt
diff --git a/.snakemake/log/2024-03-13T104321.860721.snakemake.log b/.snakemake/log/2024-03-13T104321.860721.snakemake.log
new file mode 100644
index 0000000..0325587
--- /dev/null
+++ b/.snakemake/log/2024-03-13T104321.860721.snakemake.log
@@ -0,0 +1,142 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                    count
+-------------------  -------
+M1_run_module              2
+M2_run_module              2
+all                        1
+materialize_dataset        2
+start_benchmark            1
+total                      8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:21 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 6.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 4.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 10:43:22 2024]
+Finished job 2.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D1, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 1.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D2, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 3.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 5.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 7.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 10:43:22 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 10:43:22 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T104321.860721.snakemake.log
diff --git a/.snakemake/log/2024-03-13T110317.237178.snakemake.log b/.snakemake/log/2024-03-13T110317.237178.snakemake.log
new file mode 100644
index 0000000..5bd700b
--- /dev/null
+++ b/.snakemake/log/2024-03-13T110317.237178.snakemake.log
@@ -0,0 +1,142 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                    count
+-------------------  -------
+M1_run_module              2
+M2_run_module              2
+all                        1
+materialize_dataset        2
+start_benchmark            1
+total                      8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 6.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 4.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 11:03:17 2024]
+Finished job 2.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D1, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 1.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D2, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 3.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 5.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 7.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 11:03:17 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 11:03:17 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T110317.237178.snakemake.log
diff --git a/.snakemake/log/2024-03-13T125543.434747.snakemake.log b/.snakemake/log/2024-03-13T125543.434747.snakemake.log
new file mode 100644
index 0000000..de1de11
--- /dev/null
+++ b/.snakemake/log/2024-03-13T125543.434747.snakemake.log
@@ -0,0 +1,142 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                    count
+-------------------  -------
+M1_run_module              2
+M2_run_module              2
+all                        1
+materialize_dataset        2
+start_benchmark            1
+total                      8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 4.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 5.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 7.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 6.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 12:55:43 2024]
+Finished job 2.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D2, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 3.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D1, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 1.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:55:43 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:55:43 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T125543.434747.snakemake.log
diff --git a/.snakemake/log/2024-03-13T125749.198094.snakemake.log b/.snakemake/log/2024-03-13T125749.198094.snakemake.log
new file mode 100644
index 0000000..b06ffcf
--- /dev/null
+++ b/.snakemake/log/2024-03-13T125749.198094.snakemake.log
@@ -0,0 +1,142 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                    count
+-------------------  -------
+M1_run_module              2
+M2_run_module              2
+all                        1
+materialize_dataset        2
+start_benchmark            1
+total                      8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 4.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 5.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 7.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 6.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 12:57:49 2024]
+Finished job 2.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D2, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 3.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule materialize_dataset:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: dataset=D1, params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 1.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 12:57:49 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, data/D2/default/D2_params.txt
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 12:57:49 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T125749.198094.snakemake.log
diff --git a/.snakemake/log/2024-03-13T130514.239180.snakemake.log b/.snakemake/log/2024-03-13T130514.239180.snakemake.log
new file mode 100644
index 0000000..421fa02
--- /dev/null
+++ b/.snakemake/log/2024-03-13T130514.239180.snakemake.log
@@ -0,0 +1,13 @@
+Building DAG of jobs...
+AmbiguousRuleException:
+Rules D1_materialize and D2_materialize are ambiguous for the file data/D1/default/D1_params.txt.
+Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
+Wildcards:
+	D1_materialize: dataset=D1,params=default
+	D2_materialize: dataset=D1,params=default
+Expected input files:
+	D1_materialize: log/system_profiling.txt
+	D2_materialize: log/system_profiling.txt
+Expected output files:
+	D1_materialize: data/D1/default/D1.txt.gz data/D1/default/D1.meta.json data/D1/default/D1_params.txt
+	D2_materialize: data/D1/default/D1.txt.gz data/D1/default/D1.meta.json data/D1/default/D1_params.txt
diff --git a/.snakemake/log/2024-03-13T130622.757541.snakemake.log b/.snakemake/log/2024-03-13T130622.757541.snakemake.log
new file mode 100644
index 0000000..07b24d5
--- /dev/null
+++ b/.snakemake/log/2024-03-13T130622.757541.snakemake.log
@@ -0,0 +1,143 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                count
+---------------  -------
+D1_materialize         1
+D2_materialize         1
+M1_run_module          2
+M2_run_module          2
+all                    1
+start_benchmark        1
+total                  8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:22 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:22 2024]
+Finished job 4.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:22 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:22 2024]
+Finished job 5.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:22 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:23 2024]
+Finished job 7.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:23 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, id=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:23 2024]
+Finished job 6.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:23 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 13:06:23 2024]
+Finished job 2.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:23 2024]
+localrule D2_materialize:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:23 2024]
+Finished job 3.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:23 2024]
+localrule D1_materialize:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:23 2024]
+Finished job 1.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:06:23 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, data/D1/default/D1_params.txt
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:06:23 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T130622.757541.snakemake.log
diff --git a/.snakemake/log/2024-03-13T131356.472987.snakemake.log b/.snakemake/log/2024-03-13T131356.472987.snakemake.log
new file mode 100644
index 0000000..5e178ec
--- /dev/null
+++ b/.snakemake/log/2024-03-13T131356.472987.snakemake.log
@@ -0,0 +1,143 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                count
+---------------  -------
+D1_materialize         1
+D2_materialize         1
+M1_run_module          2
+M2_run_module          2
+all                    1
+start_benchmark        1
+total                  8
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 4.
+1 of 8 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule M2_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 5.
+2 of 8 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 7.
+3 of 8 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule M1_run_module:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 6.
+4 of 8 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Wed Mar 13 13:13:56 2024]
+Finished job 2.
+5 of 8 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule D2_materialize:
+    input: log/system_profiling.txt
+    output: data/D2/default/D2.txt.gz, data/D2/default/D2.meta.json, data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 3.
+6 of 8 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule D1_materialize:
+    input: log/system_profiling.txt
+    output: data/D1/default/D1.txt.gz, data/D1/default/D1.meta.json, data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: data/D1/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: params=default
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 1.
+7 of 8 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:13:56 2024]
+localrule all:
+    input: data/D1/default/D1_params.txt, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:13:56 2024]
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T131356.472987.snakemake.log
diff --git a/.snakemake/log/2024-03-13T133713.537220.snakemake.log b/.snakemake/log/2024-03-13T133713.537220.snakemake.log
new file mode 100644
index 0000000..cc70d01
--- /dev/null
+++ b/.snakemake/log/2024-03-13T133713.537220.snakemake.log
@@ -0,0 +1,54 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                         count
+------------------------  -------
+all                             1
+stage_data_module_D1_run        1
+stage_data_module_D2_run        1
+total                           3
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:13 2024]
+localrule stage_data_module_D1_run:
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/D1_params.txt
+    wildcards: pre=out, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:13 2024]
+Finished job 1.
+1 of 3 steps (33%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:13 2024]
+localrule stage_data_module_D2_run:
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 2
+    reason: Missing output files: out/data/D2/default/D2_params.txt
+    wildcards: pre=out, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:13 2024]
+Finished job 2.
+2 of 3 steps (67%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:13 2024]
+localrule all:
+    input: out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:13 2024]
+Finished job 0.
+3 of 3 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T133713.537220.snakemake.log
diff --git a/.snakemake/log/2024-03-13T133720.351659.snakemake.log b/.snakemake/log/2024-03-13T133720.351659.snakemake.log
new file mode 100644
index 0000000..22658fb
--- /dev/null
+++ b/.snakemake/log/2024-03-13T133720.351659.snakemake.log
@@ -0,0 +1,112 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+stage_data_module_D1_run           1
+stage_data_module_D2_run           1
+stage_methods_module_M1_run        2
+stage_methods_module_M2_run        2
+total                              7
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_data_module_D1_run:
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/D1_params.txt
+    wildcards: pre=out, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 1.
+1 of 7 steps (14%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 3.
+2 of 7 steps (29%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 4.
+3 of 7 steps (43%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 6.
+4 of 7 steps (57%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 5.
+5 of 7 steps (71%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule stage_data_module_D2_run:
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 2
+    reason: Missing output files: out/data/D2/default/D2_params.txt
+    wildcards: pre=out, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 2.
+6 of 7 steps (86%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 13:37:20 2024]
+localrule all:
+    input: out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 13:37:20 2024]
+Finished job 0.
+7 of 7 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T133720.351659.snakemake.log
diff --git a/.snakemake/log/2024-03-13T150747.262258.snakemake.log b/.snakemake/log/2024-03-13T150747.262258.snakemake.log
new file mode 100644
index 0000000..e69de29
diff --git a/.snakemake/log/2024-03-13T150811.110767.snakemake.log b/.snakemake/log/2024-03-13T150811.110767.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-13T150811.110767.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-13T150815.950041.snakemake.log b/.snakemake/log/2024-03-13T150815.950041.snakemake.log
new file mode 100644
index 0000000..54e93cf
--- /dev/null
+++ b/.snakemake/log/2024-03-13T150815.950041.snakemake.log
@@ -0,0 +1,112 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+stage_data_module_D1_run           1
+stage_data_module_D2_run           1
+stage_methods_module_M1_run        2
+stage_methods_module_M2_run        2
+total                              7
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:15 2024]
+localrule stage_data_module_D1_run:
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/D1_params.txt
+    wildcards: pre=out, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 1.
+1 of 7 steps (14%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 3.
+2 of 7 steps (29%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 4.
+3 of 7 steps (43%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 6.
+4 of 7 steps (57%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 5.
+5 of 7 steps (71%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule stage_data_module_D2_run:
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 2
+    reason: Missing output files: out/data/D2/default/D2_params.txt
+    wildcards: pre=out, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 2.
+6 of 7 steps (86%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:08:16 2024]
+localrule all:
+    input: out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:08:16 2024]
+Finished job 0.
+7 of 7 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T150815.950041.snakemake.log
diff --git a/.snakemake/log/2024-03-13T152914.236273.snakemake.log b/.snakemake/log/2024-03-13T152914.236273.snakemake.log
new file mode 100644
index 0000000..d911ea2
--- /dev/null
+++ b/.snakemake/log/2024-03-13T152914.236273.snakemake.log
@@ -0,0 +1,13 @@
+Building DAG of jobs...
+AmbiguousRuleException:
+Rules stage_data_module_D2_run and stage_process_module_P2_run are ambiguous for the file out/data/D2/default/process/P2/default/D1.txt.gz.
+Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
+Wildcards:
+	stage_data_module_D2_run: name=D1,params=default/process/P2/default,pre=out
+	stage_process_module_P2_run: name=D1,params=default,pre=out/data/D2/default
+Expected input files:
+	stage_data_module_D2_run: 
+	stage_process_module_P2_run: 
+Expected output files:
+	stage_data_module_D2_run: out/data/D2/default/process/P2/default/D1.txt.gz out/data/D2/default/process/P2/default/D1.meta.json out/data/D2/default/process/P2/default/D1_params.txt
+	stage_process_module_P2_run: out/data/D2/default/process/P2/default/D1.txt.gz
diff --git a/.snakemake/log/2024-03-13T153052.126528.snakemake.log b/.snakemake/log/2024-03-13T153052.126528.snakemake.log
new file mode 100644
index 0000000..ff1e2e8
--- /dev/null
+++ b/.snakemake/log/2024-03-13T153052.126528.snakemake.log
@@ -0,0 +1,82 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+stage_methods_module_M1_run        2
+stage_methods_module_M2_run        2
+total                              5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:30:52 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:30:52 2024]
+Finished job 2.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:30:52 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:30:52 2024]
+Finished job 3.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:30:52 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:30:52 2024]
+Finished job 4.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:30:52 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:30:52 2024]
+Finished job 1.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 15:30:52 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 15:30:52 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T153052.126528.snakemake.log
diff --git a/.snakemake/log/2024-03-13T153722.882951.snakemake.log b/.snakemake/log/2024-03-13T153722.882951.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-13T153722.882951.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-13T153932.113825.snakemake.log b/.snakemake/log/2024-03-13T153932.113825.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-13T153932.113825.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-13T161746.651692.snakemake.log b/.snakemake/log/2024-03-13T161746.651692.snakemake.log
new file mode 100644
index 0000000..0154e99
--- /dev/null
+++ b/.snakemake/log/2024-03-13T161746.651692.snakemake.log
@@ -0,0 +1,82 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+stage_methods_module_M1_run        2
+stage_methods_module_M2_run        2
+total                              5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 16:17:46 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 16:17:46 2024]
+Finished job 2.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 16:17:46 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 16:17:46 2024]
+Finished job 3.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 16:17:46 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 16:17:46 2024]
+Finished job 4.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 16:17:46 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 16:17:47 2024]
+Finished job 1.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Wed Mar 13 16:17:47 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Wed Mar 13 16:17:47 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-13T161746.651692.snakemake.log
diff --git a/.snakemake/log/2024-03-14T122403.486341.snakemake.log b/.snakemake/log/2024-03-14T122403.486341.snakemake.log
new file mode 100644
index 0000000..bebe275
--- /dev/null
+++ b/.snakemake/log/2024-03-14T122403.486341.snakemake.log
@@ -0,0 +1,82 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+stage_methods_module_M1_run        2
+stage_methods_module_M2_run        2
+total                              5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:24:03 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:24:03 2024]
+Finished job 2.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:24:03 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:24:03 2024]
+Finished job 3.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:24:03 2024]
+localrule stage_methods_module_M1_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:24:03 2024]
+Finished job 4.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:24:03 2024]
+localrule stage_methods_module_M2_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, params=default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:24:03 2024]
+Finished job 1.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:24:03 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:24:03 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T122403.486341.snakemake.log
diff --git a/.snakemake/log/2024-03-14T124029.012141.snakemake.log b/.snakemake/log/2024-03-14T124029.012141.snakemake.log
new file mode 100644
index 0000000..1c49750
--- /dev/null
+++ b/.snakemake/log/2024-03-14T124029.012141.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/.snakemake/log/2024-03-14T125210.170475.snakemake.log b/.snakemake/log/2024-03-14T125210.170475.snakemake.log
new file mode 100644
index 0000000..1c49750
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125210.170475.snakemake.log
@@ -0,0 +1 @@
+Building DAG of jobs...
diff --git a/.snakemake/log/2024-03-14T125238.998424.snakemake.log b/.snakemake/log/2024-03-14T125238.998424.snakemake.log
new file mode 100644
index 0000000..37bb639
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125238.998424.snakemake.log
@@ -0,0 +1,82 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+methods_M1_default_run        2
+methods_M2_default_run        2
+total                         5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:52:39 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:52:39 2024]
+Finished job 4.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:52:39 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:52:39 2024]
+Finished job 1.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:52:39 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:52:39 2024]
+Finished job 3.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:52:39 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:52:39 2024]
+Finished job 2.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:52:39 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:52:39 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T125238.998424.snakemake.log
diff --git a/.snakemake/log/2024-03-14T125502.387647.snakemake.log b/.snakemake/log/2024-03-14T125502.387647.snakemake.log
new file mode 100644
index 0000000..242e138
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125502.387647.snakemake.log
@@ -0,0 +1,82 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+methods_M1_default_run        2
+methods_M2_default_run        2
+total                         5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:55:02 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:55:02 2024]
+Finished job 1.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:55:02 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:55:02 2024]
+Finished job 4.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:55:02 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:55:02 2024]
+Finished job 3.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:55:02 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:55:02 2024]
+Finished job 2.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:55:02 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:55:02 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T125502.387647.snakemake.log
diff --git a/.snakemake/log/2024-03-14T125737.063143.snakemake.log b/.snakemake/log/2024-03-14T125737.063143.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125737.063143.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T125859.936378.snakemake.log b/.snakemake/log/2024-03-14T125859.936378.snakemake.log
new file mode 100644
index 0000000..d486724
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125859.936378.snakemake.log
@@ -0,0 +1,16 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 17:
+Missing input files for rule all:
+    affected files:
+        out/data/D1/default/process/P2/default/data/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/data/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/process/M2/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/data/M2/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/data/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M2/default/D1.model.out.gz
diff --git a/.snakemake/log/2024-03-14T125928.702339.snakemake.log b/.snakemake/log/2024-03-14T125928.702339.snakemake.log
new file mode 100644
index 0000000..b4260ee
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125928.702339.snakemake.log
@@ -0,0 +1,16 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D1/default/process/P2/default/data/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/data/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M1/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/process/M2/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M2/default/D1.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M1/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/data/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/metrics/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/process/M2/default/D2.model.out.gz
+        out/data/D1/default/process/P2/default/data/M2/default/D1.model.out.gz
diff --git a/.snakemake/log/2024-03-14T125954.251213.snakemake.log b/.snakemake/log/2024-03-14T125954.251213.snakemake.log
new file mode 100644
index 0000000..1175dfb
--- /dev/null
+++ b/.snakemake/log/2024-03-14T125954.251213.snakemake.log
@@ -0,0 +1,399 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           2
+data_D2_default_run           2
+methods_M1_default_run        6
+methods_M2_default_run        6
+process_P1_default_run        4
+process_P2_default_run        4
+start_benchmark               1
+total                        26
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 29
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 29.
+1 of 26 steps (4%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 1.
+2 of 26 steps (8%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 11.
+3 of 26 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 9.
+4 of 26 steps (15%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 5.
+5 of 26 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 6.
+6 of 26 steps (23%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 24
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 24.
+7 of 26 steps (27%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 14
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 12:59:54 2024]
+Finished job 14.
+8 of 26 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D1.txt.gz, out/data/D2/default/D1.meta.json, out/data/D2/default/D1_params.txt
+    jobid: 18
+    reason: Missing output files: out/data/D2/default/D1.meta.json, out/data/D2/default/D1.txt.gz, out/data/D2/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:54 2024]
+Finished job 18.
+9 of 26 steps (35%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:54 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D2.txt.gz, out/data/D1/default/D2.meta.json, out/data/D1/default/D2_params.txt
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/D2.meta.json, out/data/D1/default/D2.txt.gz, out/data/D1/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 15.
+10 of 26 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 13.
+11 of 26 steps (42%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 19
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 19.
+12 of 26 steps (46%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 2.
+13 of 26 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 12.
+14 of 26 steps (54%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 20
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 20.
+15 of 26 steps (58%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D2.txt.gz
+    jobid: 25
+    reason: Missing output files: out/data/D1/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 25.
+16 of 26 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 3.
+17 of 26 steps (65%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 21
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 21.
+18 of 26 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D1.txt.gz
+    jobid: 26
+    reason: Missing output files: out/data/D2/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 26.
+19 of 26 steps (73%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 4.
+20 of 26 steps (77%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 22
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 22.
+21 of 26 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D2.txt.gz
+    jobid: 23
+    reason: Missing output files: out/data/D1/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 23.
+22 of 26 steps (85%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:55 2024]
+Finished job 10.
+23 of 26 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:55 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D1.txt.gz
+    jobid: 28
+    reason: Missing output files: out/data/D2/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:56 2024]
+Finished job 28.
+24 of 26 steps (92%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:56 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 27
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:56 2024]
+Finished job 27.
+25 of 26 steps (96%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 12:59:56 2024]
+localrule all:
+    input: out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/D2.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D2.meta.json, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D1.meta.json, out/data/D2/default/D2.meta.json, out/data/D2/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D2_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/D1.txt.gz, out/data/D2/default/D1.meta.json, out/data/D2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D1.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D2_params.txt, out/data/D2/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D1_params.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 12:59:56 2024]
+Finished job 0.
+26 of 26 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T125954.251213.snakemake.log
diff --git a/.snakemake/log/2024-03-14T130111.422943.snakemake.log b/.snakemake/log/2024-03-14T130111.422943.snakemake.log
new file mode 100644
index 0000000..5cbb09a
--- /dev/null
+++ b/.snakemake/log/2024-03-14T130111.422943.snakemake.log
@@ -0,0 +1,455 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           2
+data_D2_default_run           2
+methods_M1_default_run        8
+methods_M2_default_run        8
+process_P1_default_run        4
+process_P2_default_run        4
+start_benchmark               1
+total                        30
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 1.
+1 of 30 steps (3%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 29
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 29.
+2 of 30 steps (7%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 19
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 19.
+3 of 30 steps (10%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 14.
+4 of 30 steps (13%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 24
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 24.
+5 of 30 steps (17%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 13.
+6 of 30 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 23
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:11 2024]
+Finished job 23.
+7 of 30 steps (23%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 17
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 17.
+8 of 30 steps (27%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D2.txt.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 2.
+9 of 30 steps (30%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 10.
+10 of 30 steps (33%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 20
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 20.
+11 of 30 steps (37%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 15.
+12 of 30 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 25
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 25.
+13 of 30 steps (43%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 3.
+14 of 30 steps (47%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 11.
+15 of 30 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 21
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 21.
+16 of 30 steps (53%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 16
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 16.
+17 of 30 steps (57%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D1.txt.gz
+    jobid: 26
+    reason: Missing output files: out/data/D2/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 26.
+18 of 30 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D2.txt.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 4.
+19 of 30 steps (63%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D1.txt.gz
+    jobid: 22
+    reason: Missing output files: out/data/D2/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:12 2024]
+Finished job 22.
+20 of 30 steps (67%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:12 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 12.
+21 of 30 steps (70%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 6
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 13:01:13 2024]
+Finished job 6.
+22 of 30 steps (73%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D1.txt.gz, out/data/D2/default/D1.meta.json, out/data/D2/default/D1_params.txt
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/D1.meta.json, out/data/D2/default/D1.txt.gz, out/data/D2/default/D1_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 8.
+23 of 30 steps (77%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 9.
+24 of 30 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D2.txt.gz, out/data/D1/default/D2.meta.json, out/data/D1/default/D2_params.txt
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/D2.meta.json, out/data/D1/default/D2_params.txt, out/data/D1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 7.
+25 of 30 steps (83%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    wildcards: name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 5.
+26 of 30 steps (87%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 18
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 18.
+27 of 30 steps (90%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 28
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 28.
+28 of 30 steps (93%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 27
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 27.
+29 of 30 steps (97%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:01:13 2024]
+localrule all:
+    input: out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P2/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/D2.txt.gz, out/data/D2/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/D1.meta.json, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D2.meta.json, out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D2.meta.json, out/data/D2/default/D1.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D2_params.txt, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D1.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:01:13 2024]
+Finished job 0.
+30 of 30 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T130111.422943.snakemake.log
diff --git a/.snakemake/log/2024-03-14T130607.198301.snakemake.log b/.snakemake/log/2024-03-14T130607.198301.snakemake.log
new file mode 100644
index 0000000..f003e8e
--- /dev/null
+++ b/.snakemake/log/2024-03-14T130607.198301.snakemake.log
@@ -0,0 +1,22 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/output_params.txt
+        out/data/D1/default/output_params.txt
+        out/data/D1/default/process/P1/default/output.txt.gz
+        out/data/D1/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/process/P2/default/output.txt.gz
+        out/data/D2/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/output.meta.json
+        out/data/D2/default/process/P1/default/output.txt.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/output.meta.json
+        out/data/D1/default/output.txt.gz
+        out/data/D2/default/output.txt.gz
+        out/data/D1/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/output.txt.gz
diff --git a/.snakemake/log/2024-03-14T130628.677942.snakemake.log b/.snakemake/log/2024-03-14T130628.677942.snakemake.log
new file mode 100644
index 0000000..8fb0170
--- /dev/null
+++ b/.snakemake/log/2024-03-14T130628.677942.snakemake.log
@@ -0,0 +1,22 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/output.txt.gz
+        out/data/D2/default/output_params.txt
+        out/data/D2/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/output.meta.json
+        out/data/D2/default/process/P1/default/output.txt.gz
+        out/data/D2/default/process/P2/default/output.txt.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/output_params.txt
+        out/data/D1/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/output.txt.gz
+        out/data/D2/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/output.txt.gz
+        out/data/D2/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P1/default/output.txt.gz
+        out/data/D2/default/output.meta.json
diff --git a/.snakemake/log/2024-03-14T130841.763216.snakemake.log b/.snakemake/log/2024-03-14T130841.763216.snakemake.log
new file mode 100644
index 0000000..738e489
--- /dev/null
+++ b/.snakemake/log/2024-03-14T130841.763216.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/D1.meta.json
+        out/data/D2/default/D1_params.txt
+        out/data/D1/default/D2.txt.gz
+        out/data/D1/default/D2_params.txt
+        out/data/D1/default/D2.meta.json
+        out/data/D2/default/D1.txt.gz
diff --git a/.snakemake/log/2024-03-14T131356.196612.snakemake.log b/.snakemake/log/2024-03-14T131356.196612.snakemake.log
new file mode 100644
index 0000000..ca82150
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131356.196612.snakemake.log
@@ -0,0 +1,22 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/output_params.txt
+        out/data/D1/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/process/P1/default/output.txt.gz
+        out/data/D2/default/process/P2/default/output.txt.gz
+        out/data/D2/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/process/P1/default/output.txt.gz
+        out/data/D1/default/output.txt.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/output.meta.json
+        out/data/D1/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/output.txt.gz
+        out/data/D2/default/output.txt.gz
+        out/data/D2/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/output.meta.json
+        out/data/D1/default/output_params.txt
diff --git a/.snakemake/log/2024-03-14T131416.514746.snakemake.log b/.snakemake/log/2024-03-14T131416.514746.snakemake.log
new file mode 100644
index 0000000..bee43d7
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131416.514746.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/D1_params.txt
+        out/data/D2/default/D1.meta.json
+        out/data/D1/default/D2_params.txt
+        out/data/D1/default/D2.txt.gz
+        out/data/D2/default/D1.txt.gz
+        out/data/D1/default/D2.meta.json
diff --git a/.snakemake/log/2024-03-14T131443.225073.snakemake.log b/.snakemake/log/2024-03-14T131443.225073.snakemake.log
new file mode 100644
index 0000000..6f03245
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131443.225073.snakemake.log
@@ -0,0 +1,22 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/output.meta.json
+        out/data/D1/default/output.meta.json
+        out/data/D1/default/process/P2/default/output.txt.gz
+        out/data/D2/default/output.txt.gz
+        out/data/D2/default/process/P1/default/methods/M1/default/output.model.out.gz
+        out/data/D2/default/process/P2/default/output.txt.gz
+        out/data/D1/default/process/P1/default/output.txt.gz
+        out/data/D2/default/process/P1/default/output.txt.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/output.model.out.gz
+        out/data/D1/default/output_params.txt
+        out/data/D2/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D2/default/output_params.txt
+        out/data/D1/default/output.txt.gz
+        out/data/D1/default/process/P1/default/methods/M2/default/output.model.out.gz
+        out/data/D1/default/process/P1/default/methods/M1/default/output.model.out.gz
diff --git a/.snakemake/log/2024-03-14T131506.738217.snakemake.log b/.snakemake/log/2024-03-14T131506.738217.snakemake.log
new file mode 100644
index 0000000..79cf1dc
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131506.738217.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/D1.meta.json
+        out/data/D2/default/D1.txt.gz
+        out/data/D1/default/D2.meta.json
+        out/data/D1/default/D2_params.txt
+        out/data/D1/default/D2.txt.gz
+        out/data/D2/default/D1_params.txt
diff --git a/.snakemake/log/2024-03-14T131645.788523.snakemake.log b/.snakemake/log/2024-03-14T131645.788523.snakemake.log
new file mode 100644
index 0000000..ed0198d
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131645.788523.snakemake.log
@@ -0,0 +1,7 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D1/default/D2.meta.json
+        out/data/D1/default/D2_params.txt
+        out/data/D1/default/D2.txt.gz
diff --git a/.snakemake/log/2024-03-14T131914.281802.snakemake.log b/.snakemake/log/2024-03-14T131914.281802.snakemake.log
new file mode 100644
index 0000000..f6d6415
--- /dev/null
+++ b/.snakemake/log/2024-03-14T131914.281802.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Error:
+  TypeError: expected string or bytes-like object, got 'Wildcards'
+Wildcards:
+
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 21, in <lambda>
+  File "/usr/lib/python3.11/re/__init__.py", line 166, in match (rule all, line 22, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T132033.922136.snakemake.log b/.snakemake/log/2024-03-14T132033.922136.snakemake.log
new file mode 100644
index 0000000..46b857a
--- /dev/null
+++ b/.snakemake/log/2024-03-14T132033.922136.snakemake.log
@@ -0,0 +1,28 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D1/default/D2.meta.json
+        out/data/D1/default/D2_params.txt
+        out/data/D2/default/process/P1/default/methods/M1/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D1/default/<function <lambda> at 0x78873a4e98a0>.meta.json
+        out/data/D2/default/process/P2/default/methods/M2/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D1/default/process/P1/default/methods/M2/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D2/default/D1.txt.gz
+        out/data/D2/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D2/default/<function <lambda> at 0x78873a4e98a0>_params.txt
+        out/data/D2/default/D1.meta.json
+        out/data/D2/default/<function <lambda> at 0x78873a4e98a0>.meta.json
+        out/data/D2/default/process/P2/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D1/default/process/P2/default/methods/M1/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D1/default/process/P1/default/methods/M1/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D2/default/process/P2/default/methods/M1/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D1/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D1/default/D2.txt.gz
+        out/data/D1/default/process/P2/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D1/default/process/P1/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D2/default/process/P1/default/methods/M2/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
+        out/data/D1/default/<function <lambda> at 0x78873a4e98a0>_params.txt
+        out/data/D2/default/D1_params.txt
+        out/data/D2/default/process/P1/default/<function <lambda> at 0x78873a4e98a0>.txt.gz
+        out/data/D1/default/process/P2/default/methods/M2/default/<function <lambda> at 0x78873a4e98a0>.model.out.gz
diff --git a/.snakemake/log/2024-03-14T132155.787935.snakemake.log b/.snakemake/log/2024-03-14T132155.787935.snakemake.log
new file mode 100644
index 0000000..30979fb
--- /dev/null
+++ b/.snakemake/log/2024-03-14T132155.787935.snakemake.log
@@ -0,0 +1,10 @@
+Building DAG of jobs...
+MissingInputException in rule all in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 18:
+Missing input files for rule all:
+    affected files:
+        out/data/D2/default/D1_params.txt
+        out/data/D1/default/D2.txt.gz
+        out/data/D2/default/D1.meta.json
+        out/data/D1/default/D2_params.txt
+        out/data/D2/default/D1.txt.gz
+        out/data/D1/default/D2.meta.json
diff --git a/.snakemake/log/2024-03-14T133326.667956.snakemake.log b/.snakemake/log/2024-03-14T133326.667956.snakemake.log
new file mode 100644
index 0000000..13cb2ce
--- /dev/null
+++ b/.snakemake/log/2024-03-14T133326.667956.snakemake.log
@@ -0,0 +1,255 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:26 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:26 2024]
+Finished job 13.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:26 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:26 2024]
+Finished job 4.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:26 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:26 2024]
+Finished job 14.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:26 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 13:33:26 2024]
+Finished job 2.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:26 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 3.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json, out/data/D1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 1.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 9.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 5.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 15.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 10.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 6.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 7.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 12.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 11.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 8.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:33:27 2024]
+localrule all:
+    input: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:33:27 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T133326.667956.snakemake.log
diff --git a/.snakemake/log/2024-03-14T133540.914407.snakemake.log b/.snakemake/log/2024-03-14T133540.914407.snakemake.log
new file mode 100644
index 0000000..be586c8
--- /dev/null
+++ b/.snakemake/log/2024-03-14T133540.914407.snakemake.log
@@ -0,0 +1,538 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                            count
+---------------------------  -------
+all                                1
+data_D1_default_run                1
+data_D2_default_run                1
+methods_M1_default_run             8
+methods_M2_-d1__-e_1_run           8
+methods_M2_-d1__-e_2_run           8
+process_P1_-a_0__-b_0_1_run        2
+process_P1_-a_1__-b_0_1_run        2
+process_P2_-a_0__-c_0_run          2
+process_P2_-a_1__-c_0_1_run        2
+start_benchmark                    1
+total                             36
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:40 2024]
+localrule process_P1_-a_0__-b_0_1_run:
+    output: out/data/D2/default/process/P1/-a_0__-b_0_1/D2.txt.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P1/-a_0__-b_0_1/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 3.
+1 of 36 steps (3%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/-a_0__-c_0/methods/M1/default/D1.model.out.gz
+    jobid: 22
+    reason: Missing output files: out/data/D1/default/process/P2/-a_0__-c_0/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_0__-c_0, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 22.
+2 of 36 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    jobid: 32
+    reason: Missing output files: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_0__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 32.
+3 of 36 steps (8%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/-a_0__-c_0/methods/M1/default/D2.model.out.gz
+    jobid: 27
+    reason: Missing output files: out/data/D2/default/process/P2/-a_0__-c_0/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_0__-c_0, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 27.
+4 of 36 steps (11%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M1/default/D2.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_1__-c_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 8.
+5 of 36 steps (14%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule process_P2_-a_1__-c_0_1_run:
+    output: out/data/D2/default/process/P2/-a_1__-c_0_1/D2.txt.gz
+    jobid: 17
+    reason: Missing output files: out/data/D2/default/process/P2/-a_1__-c_0_1/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 17.
+6 of 36 steps (17%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule process_P2_-a_1__-c_0_1_run:
+    output: out/data/D1/default/process/P2/-a_1__-c_0_1/D1.txt.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P2/-a_1__-c_0_1/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 2.
+7 of 36 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    jobid: 31
+    reason: Missing output files: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_1__-c_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 31.
+8 of 36 steps (22%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    jobid: 21
+    reason: Missing output files: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_1__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 21.
+9 of 36 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M1/default/D1.model.out.gz
+    jobid: 16
+    reason: Missing output files: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_1__-c_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 16.
+10 of 36 steps (28%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    jobid: 26
+    reason: Missing output files: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_0__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 26.
+11 of 36 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule process_P1_-a_1__-b_0_1_run:
+    output: out/data/D1/default/process/P1/-a_1__-b_0_1/D1.txt.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P1/-a_1__-b_0_1/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 7.
+12 of 36 steps (33%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_1__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:41 2024]
+Finished job 13.
+13 of 36 steps (36%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:41 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M1/default/D2.model.out.gz
+    jobid: 20
+    reason: Missing output files: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_1__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 20.
+14 of 36 steps (39%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M1/default/D1.model.out.gz
+    jobid: 30
+    reason: Missing output files: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_0__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 30.
+15 of 36 steps (42%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_1__-c_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 6.
+16 of 36 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule process_P1_-a_0__-b_0_1_run:
+    output: out/data/D1/default/process/P1/-a_0__-b_0_1/D1.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/-a_0__-b_0_1/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 15.
+17 of 36 steps (47%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D2.model.out.gz
+    jobid: 25
+    reason: Missing output files: out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_0__-c_0, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 25.
+18 of 36 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    jobid: 35
+    reason: Missing output files: out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_1__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 35.
+19 of 36 steps (53%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D2.model.out.gz
+    jobid: 24
+    reason: Missing output files: out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/-a_0__-c_0, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 24.
+20 of 36 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    jobid: 34
+    reason: Missing output files: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_1__-c_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 34.
+21 of 36 steps (58%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_0__-c_0, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 10.
+22 of 36 steps (61%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M1/default/D1.model.out.gz
+    jobid: 29
+    reason: Missing output files: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_1__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 29.
+23 of 36 steps (64%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M1/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_0__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 4.
+24 of 36 steps (67%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule process_P2_-a_0__-c_0_run:
+    output: out/data/D2/default/process/P2/-a_0__-c_0/D2.txt.gz
+    jobid: 23
+    reason: Missing output files: out/data/D2/default/process/P2/-a_0__-c_0/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 23.
+25 of 36 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D1.model.out.gz
+    jobid: 33
+    reason: Missing output files: out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_0__-c_0, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 33.
+26 of 36 steps (72%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/-a_1__-c_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:42 2024]
+Finished job 9.
+27 of 36 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:42 2024]
+localrule process_P2_-a_0__-c_0_run:
+    output: out/data/D1/default/process/P2/-a_0__-c_0/D1.txt.gz
+    jobid: 18
+    reason: Missing output files: out/data/D1/default/process/P2/-a_0__-c_0/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 18.
+28 of 36 steps (78%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule methods_M2_-d1__-e_2_run:
+    output: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    jobid: 28
+    reason: Missing output files: out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/-a_0__-b_0_1, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 28.
+29 of 36 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    jobid: 19
+    reason: Missing output files: out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_0__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 19.
+30 of 36 steps (83%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule methods_M2_-d1__-e_1_run:
+    output: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/-a_1__-b_0_1, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 5.
+31 of 36 steps (86%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule process_P1_-a_1__-b_0_1_run:
+    output: out/data/D2/default/process/P1/-a_1__-b_0_1/D2.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D2/default/process/P1/-a_1__-b_0_1/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 1.
+32 of 36 steps (89%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 12
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 13:35:43 2024]
+Finished job 12.
+33 of 36 steps (92%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 11.
+34 of 36 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 14.
+35 of 36 steps (97%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 13:35:43 2024]
+localrule all:
+    input: out/data/D2/default/process/P1/-a_1__-b_0_1/D2.txt.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/D1.txt.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/D2.txt.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/D1.txt.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/-a_0__-b_0_1/D1.txt.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/D2.txt.gz, out/data/D1/default/process/P2/-a_0__-c_0/D1.txt.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/-a_0__-c_0/D2.txt.gz, out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D2/default/process/P2/-a_0__-c_0/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/-a_1__-b_0_1/D2.txt.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/D1.txt.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/D2.txt.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/D1.txt.gz, out/data/D2/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/D1.txt.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D1/default/process/P1/-a_1__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/D1.txt.gz, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/D2.txt.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/-a_1__-c_0_1/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/-a_0__-c_0/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/-a_0__-c_0/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_1/D1.model.out.gz, out/data/D2/default/process/P2/-a_0__-c_0/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_1/D2.model.out.gz, out/data/D1/default/process/P1/-a_0__-b_0_1/methods/M2/-d1__-e_2/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P2/-a_0__-c_0/methods/M2/-d1__-e_2/D2.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/-a_0__-b_0_1/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/-a_1__-c_0_1/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 13:35:43 2024]
+Finished job 0.
+36 of 36 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T133540.914407.snakemake.log
diff --git a/.snakemake/log/2024-03-14T142537.917672.snakemake.log b/.snakemake/log/2024-03-14T142537.917672.snakemake.log
new file mode 100644
index 0000000..c70455f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142537.917672.snakemake.log
@@ -0,0 +1,255 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:37 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 1.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 9.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 2
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 2.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 14.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 12.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 3.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 15.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 10.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 4.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 5.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 13.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 8
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 14:25:38 2024]
+Finished job 8.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 11
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 11.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/D2_params.txt, out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:38 2024]
+Finished job 7.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:38 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:39 2024]
+Finished job 6.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 14:25:39 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1_params.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 14:25:39 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T142537.917672.snakemake.log
diff --git a/.snakemake/log/2024-03-14T142607.581424.snakemake.log b/.snakemake/log/2024-03-14T142607.581424.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142607.581424.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T142616.882833.snakemake.log b/.snakemake/log/2024-03-14T142616.882833.snakemake.log
new file mode 100644
index 0000000..465da51
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142616.882833.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule process_P1_default_run.
diff --git a/.snakemake/log/2024-03-14T142716.652008.snakemake.log b/.snakemake/log/2024-03-14T142716.652008.snakemake.log
new file mode 100644
index 0000000..d117bfe
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142716.652008.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Cyclic dependency on rule process_P1_default_run.
diff --git a/.snakemake/log/2024-03-14T142800.690893.snakemake.log b/.snakemake/log/2024-03-14T142800.690893.snakemake.log
new file mode 100644
index 0000000..9447fc6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142800.690893.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule process_P2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Cyclic dependency on rule process_P2_default_run.
diff --git a/.snakemake/log/2024-03-14T142836.337550.snakemake.log b/.snakemake/log/2024-03-14T142836.337550.snakemake.log
new file mode 100644
index 0000000..2c3d081
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142836.337550.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+MissingInputException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Missing input files for rule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    affected files:
+        out/data/D2/default/process/P1/default/methods/M2/default/D2_params.txt
+        out/data/D2/default/process/P1/default/methods/M2/default/D2.txt.gz
+        out/data/D2/default/process/P1/default/methods/M2/default/D2.meta.json
diff --git a/.snakemake/log/2024-03-14T142844.696969.snakemake.log b/.snakemake/log/2024-03-14T142844.696969.snakemake.log
new file mode 100644
index 0000000..d117bfe
--- /dev/null
+++ b/.snakemake/log/2024-03-14T142844.696969.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Cyclic dependency on rule process_P1_default_run.
diff --git a/.snakemake/log/2024-03-14T143016.674481.snakemake.log b/.snakemake/log/2024-03-14T143016.674481.snakemake.log
new file mode 100644
index 0000000..329f0a7
--- /dev/null
+++ b/.snakemake/log/2024-03-14T143016.674481.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+MissingInputException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Missing input files for rule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    affected files:
+        out/data/D2/default/process/P2/default/methods/M2/default/D2_params.txt
+        out/data/D2/default/process/P2/default/methods/M2/default/D2.meta.json
+        out/data/D2/default/process/P2/default/methods/M2/default/D2.txt.gz
diff --git a/.snakemake/log/2024-03-14T143118.616371.snakemake.log b/.snakemake/log/2024-03-14T143118.616371.snakemake.log
new file mode 100644
index 0000000..e5ae501
--- /dev/null
+++ b/.snakemake/log/2024-03-14T143118.616371.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Wildcards in input files cannot be determined from output files: (rule methods_M1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T143131.175390.snakemake.log b/.snakemake/log/2024-03-14T143131.175390.snakemake.log
new file mode 100644
index 0000000..1f3637b
--- /dev/null
+++ b/.snakemake/log/2024-03-14T143131.175390.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Wildcards in input files cannot be determined from output files: (rule process_P1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'stage'
diff --git a/.snakemake/log/2024-03-14T144929.156488.snakemake.log b/.snakemake/log/2024-03-14T144929.156488.snakemake.log
new file mode 100644
index 0000000..d434cc4
--- /dev/null
+++ b/.snakemake/log/2024-03-14T144929.156488.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Wildcards in input files cannot be determined from output files: (rule methods_M2_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T145046.009904.snakemake.log b/.snakemake/log/2024-03-14T145046.009904.snakemake.log
new file mode 100644
index 0000000..1563951
--- /dev/null
+++ b/.snakemake/log/2024-03-14T145046.009904.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Wildcards in input files cannot be determined from output files: (rule process_P1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T145951.798101.snakemake.log b/.snakemake/log/2024-03-14T145951.798101.snakemake.log
new file mode 100644
index 0000000..436b381
--- /dev/null
+++ b/.snakemake/log/2024-03-14T145951.798101.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Wildcards in input files cannot be determined from output files: (rule methods_M1_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T150102.307922.snakemake.log b/.snakemake/log/2024-03-14T150102.307922.snakemake.log
new file mode 100644
index 0000000..436b381
--- /dev/null
+++ b/.snakemake/log/2024-03-14T150102.307922.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Wildcards in input files cannot be determined from output files: (rule methods_M1_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T150148.463498.snakemake.log b/.snakemake/log/2024-03-14T150148.463498.snakemake.log
new file mode 100644
index 0000000..94a9f9a
--- /dev/null
+++ b/.snakemake/log/2024-03-14T150148.463498.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Wildcards in input files cannot be determined from output files: (rule methods_M2_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T150910.862226.snakemake.log b/.snakemake/log/2024-03-14T150910.862226.snakemake.log
new file mode 100644
index 0000000..937ae88
--- /dev/null
+++ b/.snakemake/log/2024-03-14T150910.862226.snakemake.log
@@ -0,0 +1,255 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:10 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:10 2024]
+Finished job 10.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:10 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 4
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 15:09:10 2024]
+Finished job 4.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:10 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 7.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 3.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 1.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 11.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 2
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 2.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 5.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 12.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 8.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 6.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 14.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 13.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 9.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 15.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:09:11 2024]
+localrule all:
+    input: out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:09:11 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T150910.862226.snakemake.log
diff --git a/.snakemake/log/2024-03-14T151418.491135.snakemake.log b/.snakemake/log/2024-03-14T151418.491135.snakemake.log
new file mode 100644
index 0000000..150632e
--- /dev/null
+++ b/.snakemake/log/2024-03-14T151418.491135.snakemake.log
@@ -0,0 +1,208 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+total                        13
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 6
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 6.
+1 of 13 steps (8%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 14
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 14.
+2 of 13 steps (15%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 10
+    reason: Updated input files: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 10.
+3 of 13 steps (23%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 1
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 1.
+4 of 13 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 5
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 5.
+5 of 13 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 13
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:18 2024]
+Finished job 13.
+6 of 13 steps (46%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:18 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 15
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 15.
+7 of 13 steps (54%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 8
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 8.
+8 of 13 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 7
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 7.
+9 of 13 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 11
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 11.
+10 of 13 steps (77%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 4
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 4.
+11 of 13 steps (85%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 3
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 3.
+12 of 13 steps (92%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:14:19 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:14:19 2024]
+Finished job 0.
+13 of 13 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T151418.491135.snakemake.log
diff --git a/.snakemake/log/2024-03-14T152249.352527.snakemake.log b/.snakemake/log/2024-03-14T152249.352527.snakemake.log
new file mode 100644
index 0000000..39335fb
--- /dev/null
+++ b/.snakemake/log/2024-03-14T152249.352527.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Wildcards in input files cannot be determined from output files: (rule process_P1_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-14T152558.766263.snakemake.log b/.snakemake/log/2024-03-14T152558.766263.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T152558.766263.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T152842.605254.snakemake.log b/.snakemake/log/2024-03-14T152842.605254.snakemake.log
new file mode 100644
index 0000000..f277bf8
--- /dev/null
+++ b/.snakemake/log/2024-03-14T152842.605254.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T152940.447426.snakemake.log b/.snakemake/log/2024-03-14T152940.447426.snakemake.log
new file mode 100644
index 0000000..6327bb9
--- /dev/null
+++ b/.snakemake/log/2024-03-14T152940.447426.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Cyclic dependency on rule methods_M1_default_run.
diff --git a/.snakemake/log/2024-03-14T153106.181918.snakemake.log b/.snakemake/log/2024-03-14T153106.181918.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153106.181918.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T153156.720661.snakemake.log b/.snakemake/log/2024-03-14T153156.720661.snakemake.log
new file mode 100644
index 0000000..94cc599
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153156.720661.snakemake.log
@@ -0,0 +1,7 @@
+Building DAG of jobs...
+MissingInputException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Missing input files for rule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    affected files:
+        log/system_profiling.log
diff --git a/.snakemake/log/2024-03-14T153212.435474.snakemake.log b/.snakemake/log/2024-03-14T153212.435474.snakemake.log
new file mode 100644
index 0000000..6a1dd81
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153212.435474.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 15:32:12 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 14.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 6.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 10.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 1.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 13.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:12 2024]
+Finished job 5.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:12 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 9.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 12.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 4.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 8.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 15.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 7.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 11
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 11.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 3.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:32:13 2024]
+localrule all:
+    input: out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1.meta.json, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:32:13 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T153212.435474.snakemake.log
diff --git a/.snakemake/log/2024-03-14T153311.698898.snakemake.log b/.snakemake/log/2024-03-14T153311.698898.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153311.698898.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T153839.565827.snakemake.log b/.snakemake/log/2024-03-14T153839.565827.snakemake.log
new file mode 100644
index 0000000..f1eb5f4
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153839.565827.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule process_P2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Error:
+  TypeError: format_input_templates_to_be_expanded() got an unexpected keyword argument 'wildcards'
+Wildcards:
+  pre=out/data/D1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 102, in <lambda> (rule process_P2_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T153904.956430.snakemake.log b/.snakemake/log/2024-03-14T153904.956430.snakemake.log
new file mode 100644
index 0000000..b62cd5f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153904.956430.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Error:
+  TypeError: format_input_templates_to_be_expanded() got an unexpected keyword argument 'wildcards'
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 102, in <lambda> (rule methods_M1_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T153925.771332.snakemake.log b/.snakemake/log/2024-03-14T153925.771332.snakemake.log
new file mode 100644
index 0000000..b62cd5f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T153925.771332.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Error:
+  TypeError: format_input_templates_to_be_expanded() got an unexpected keyword argument 'wildcards'
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 102, in <lambda> (rule methods_M1_default_run, line 155, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T154013.525590.snakemake.log b/.snakemake/log/2024-03-14T154013.525590.snakemake.log
new file mode 100644
index 0000000..2736fd9
--- /dev/null
+++ b/.snakemake/log/2024-03-14T154013.525590.snakemake.log
@@ -0,0 +1,196 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+total                        13
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 6
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:13 2024]
+Finished job 6.
+1 of 13 steps (8%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule process_P2_default_run:
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 13
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:13 2024]
+Finished job 13.
+2 of 13 steps (15%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 8
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:13 2024]
+Finished job 8.
+3 of 13 steps (23%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule process_P2_default_run:
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 14
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:13 2024]
+Finished job 14.
+4 of 13 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule methods_M1_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 9
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:13 2024]
+Finished job 9.
+5 of 13 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:13 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 15
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 15.
+6 of 13 steps (46%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 11
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 11.
+7 of 13 steps (54%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule process_P1_default_run:
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 10
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 10.
+8 of 13 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule methods_M2_default_run:
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 2
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 2.
+9 of 13 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule methods_M2_default_run:
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 12
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 12.
+10 of 13 steps (77%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule process_P1_default_run:
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 3
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 3.
+11 of 13 steps (85%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule methods_M1_default_run:
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 1
+    reason: Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 1.
+12 of 13 steps (92%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 15:40:14 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 15:40:14 2024]
+Finished job 0.
+13 of 13 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T154013.525590.snakemake.log
diff --git a/.snakemake/log/2024-03-14T154116.669794.snakemake.log b/.snakemake/log/2024-03-14T154116.669794.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T154116.669794.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T154255.336478.snakemake.log b/.snakemake/log/2024-03-14T154255.336478.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T154255.336478.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T155125.386040.snakemake.log b/.snakemake/log/2024-03-14T155125.386040.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T155125.386040.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T155334.395544.snakemake.log b/.snakemake/log/2024-03-14T155334.395544.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T155334.395544.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T155344.825372.snakemake.log b/.snakemake/log/2024-03-14T155344.825372.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T155344.825372.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160520.131536.snakemake.log b/.snakemake/log/2024-03-14T160520.131536.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160520.131536.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160554.643105.snakemake.log b/.snakemake/log/2024-03-14T160554.643105.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160554.643105.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160609.903444.snakemake.log b/.snakemake/log/2024-03-14T160609.903444.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160609.903444.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160704.858346.snakemake.log b/.snakemake/log/2024-03-14T160704.858346.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160704.858346.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160725.078592.snakemake.log b/.snakemake/log/2024-03-14T160725.078592.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160725.078592.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T160747.176185.snakemake.log b/.snakemake/log/2024-03-14T160747.176185.snakemake.log
new file mode 100644
index 0000000..a058195
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160747.176185.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:07:47 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 5.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 9.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 12.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 4.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 15.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 7.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 3.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 11
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 11.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 14.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 1
+    reason: Missing output files: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:47 2024]
+Finished job 1.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:47 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:48 2024]
+Finished job 10.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:48 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:48 2024]
+Finished job 8.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:48 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:48 2024]
+Finished job 13.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:48 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:48 2024]
+Finished job 6.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:07:48 2024]
+localrule all:
+    input: out/data/D2/default/D2.meta.json, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/D2_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:07:48 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T160747.176185.snakemake.log
diff --git a/.snakemake/log/2024-03-14T160759.331569.snakemake.log b/.snakemake/log/2024-03-14T160759.331569.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160759.331569.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160830.982186.snakemake.log b/.snakemake/log/2024-03-14T160830.982186.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160830.982186.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T160916.155879.snakemake.log b/.snakemake/log/2024-03-14T160916.155879.snakemake.log
new file mode 100644
index 0000000..52bab09
--- /dev/null
+++ b/.snakemake/log/2024-03-14T160916.155879.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:09:16 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 9.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 12.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 4.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json, out/data/D1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 8.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 15.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 5.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 7.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 1.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 3.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:16 2024]
+Finished job 11.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:16 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:17 2024]
+Finished job 10.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:17 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:17 2024]
+Finished job 14.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:17 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:17 2024]
+Finished job 13.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:17 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:17 2024]
+Finished job 6.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:09:17 2024]
+localrule all:
+    input: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P1/default/D2.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:09:17 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T160916.155879.snakemake.log
diff --git a/.snakemake/log/2024-03-14T161002.065257.snakemake.log b/.snakemake/log/2024-03-14T161002.065257.snakemake.log
new file mode 100644
index 0000000..b20b749
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161002.065257.snakemake.log
@@ -0,0 +1,86 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+process_P1_default_run        2
+process_P2_default_run        2
+total                         5
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:10:02 2024]
+localrule process_P2_default_run:
+    input: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 4
+    reason: Updated input files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:10:02 2024]
+Finished job 4.
+1 of 5 steps (20%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:10:02 2024]
+localrule process_P1_default_run:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 6
+    reason: Updated input files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:10:02 2024]
+Finished job 6.
+2 of 5 steps (40%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:10:02 2024]
+localrule process_P1_default_run:
+    input: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 7
+    reason: Updated input files: out/data/D2/default/D2_params.txt, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:10:02 2024]
+Finished job 7.
+3 of 5 steps (60%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:10:02 2024]
+localrule process_P2_default_run:
+    input: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 3
+    reason: Updated input files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:10:02 2024]
+Finished job 3.
+4 of 5 steps (80%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:10:02 2024]
+localrule all:
+    input: out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/D2_params.txt
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P1/default/D1.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:10:02 2024]
+Finished job 0.
+5 of 5 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T161002.065257.snakemake.log
diff --git a/.snakemake/log/2024-03-14T161014.255436.snakemake.log b/.snakemake/log/2024-03-14T161014.255436.snakemake.log
new file mode 100644
index 0000000..0e62396
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161014.255436.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M1_default_run.
diff --git a/.snakemake/log/2024-03-14T161056.953071.snakemake.log b/.snakemake/log/2024-03-14T161056.953071.snakemake.log
new file mode 100644
index 0000000..0e62396
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161056.953071.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M1_default_run.
diff --git a/.snakemake/log/2024-03-14T161154.829633.snakemake.log b/.snakemake/log/2024-03-14T161154.829633.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161154.829633.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T161701.880320.snakemake.log b/.snakemake/log/2024-03-14T161701.880320.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161701.880320.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T161712.205847.snakemake.log b/.snakemake/log/2024-03-14T161712.205847.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161712.205847.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T161718.455000.snakemake.log b/.snakemake/log/2024-03-14T161718.455000.snakemake.log
new file mode 100644
index 0000000..5e131b6
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161718.455000.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 94:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T161748.181177.snakemake.log b/.snakemake/log/2024-03-14T161748.181177.snakemake.log
new file mode 100644
index 0000000..600f77f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T161748.181177.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T162202.162298.snakemake.log b/.snakemake/log/2024-03-14T162202.162298.snakemake.log
new file mode 100644
index 0000000..600f77f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162202.162298.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T162252.346526.snakemake.log b/.snakemake/log/2024-03-14T162252.346526.snakemake.log
new file mode 100644
index 0000000..429af3f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162252.346526.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Cyclic dependency on rule methods_M1_default_run.
diff --git a/.snakemake/log/2024-03-14T162346.370984.snakemake.log b/.snakemake/log/2024-03-14T162346.370984.snakemake.log
new file mode 100644
index 0000000..429af3f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162346.370984.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Cyclic dependency on rule methods_M1_default_run.
diff --git a/.snakemake/log/2024-03-14T162407.717451.snakemake.log b/.snakemake/log/2024-03-14T162407.717451.snakemake.log
new file mode 100644
index 0000000..600f77f
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162407.717451.snakemake.log
@@ -0,0 +1,3 @@
+Building DAG of jobs...
+CyclicGraphException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Cyclic dependency on rule methods_M2_default_run.
diff --git a/.snakemake/log/2024-03-14T162433.205078.snakemake.log b/.snakemake/log/2024-03-14T162433.205078.snakemake.log
new file mode 100644
index 0000000..295f4f9
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162433.205078.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:24:33 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 14.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 6.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 1.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 3.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 13.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 9.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 5.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:33 2024]
+Finished job 12.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:33 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 10
+    reason: Missing output files: out/data/D2/default/D2_params.txt, out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 10.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 4.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 8.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 15.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt; Set of input files has changed since last execution
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 7.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 11.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:24:34 2024]
+localrule all:
+    input: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1.meta.json
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:24:34 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T162433.205078.snakemake.log
diff --git a/.snakemake/log/2024-03-14T162707.977496.snakemake.log b/.snakemake/log/2024-03-14T162707.977496.snakemake.log
new file mode 100644
index 0000000..3971fca
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162707.977496.snakemake.log
@@ -0,0 +1,2 @@
+Building DAG of jobs...
+Nothing to be done (all requested files are present and up to date).
diff --git a/.snakemake/log/2024-03-14T162714.901875.snakemake.log b/.snakemake/log/2024-03-14T162714.901875.snakemake.log
new file mode 100644
index 0000000..c2fb4f1
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162714.901875.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:14 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:27:14 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:14 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 14.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 6
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 6.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 1.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 10.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 8.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 3.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 13.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 5.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 9.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 12.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 15.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 7.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 4.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 11.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:15 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:15 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T162714.901875.snakemake.log
diff --git a/.snakemake/log/2024-03-14T162753.336457.snakemake.log b/.snakemake/log/2024-03-14T162753.336457.snakemake.log
new file mode 100644
index 0000000..62d7850
--- /dev/null
+++ b/.snakemake/log/2024-03-14T162753.336457.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:27:53 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 5
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 5.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 9
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 9.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 12.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 4.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 8.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 15.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 13
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 13.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:53 2024]
+Finished job 11.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:53 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 7.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 6.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 3.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 14.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 10.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 1.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:27:54 2024]
+localrule all:
+    input: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/D1.txt.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D2/default/D2.meta.json, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:27:54 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T162753.336457.snakemake.log
diff --git a/.snakemake/log/2024-03-14T163013.516825.snakemake.log b/.snakemake/log/2024-03-14T163013.516825.snakemake.log
new file mode 100644
index 0000000..05723aa
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163013.516825.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'outputs'
+Wildcards:
+  pre=out/data/D2/default/process/P1/default
+  name=D2
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 104, in <lambda> (rule methods_M2_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163049.838022.snakemake.log b/.snakemake/log/2024-03-14T163049.838022.snakemake.log
new file mode 100644
index 0000000..cd35557
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163049.838022.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'output'
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 104, in <lambda> (rule methods_M1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163101.934544.snakemake.log b/.snakemake/log/2024-03-14T163101.934544.snakemake.log
new file mode 100644
index 0000000..4293058
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163101.934544.snakemake.log
@@ -0,0 +1,11 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'pre'
+Wildcards:
+  pre=out/data/D2/default/process/P1/default
+  name=D2
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 104, in <lambda>
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/snakemake.py", line 41, in format_input_templates_to_be_expanded
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/src/formatter.py", line 51, in format_input_templates_to_be_expanded (rule methods_M1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163138.439586.snakemake.log b/.snakemake/log/2024-03-14T163138.439586.snakemake.log
new file mode 100644
index 0000000..f5cb9aa
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163138.439586.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Thu Mar 14 16:31:38 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 5.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 9.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 12.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 4
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 4.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 8.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:38 2024]
+Finished job 15.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:38 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 7
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 7.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 6.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 3.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 11.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 10
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 10.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 14
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 14.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 13.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 1.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Thu Mar 14 16:31:39 2024]
+localrule all:
+    input: out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/D1.txt.gz
+    resources: tmpdir=/tmp
+
+[Thu Mar 14 16:31:39 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-14T163138.439586.snakemake.log
diff --git a/.snakemake/log/2024-03-14T163231.507025.snakemake.log b/.snakemake/log/2024-03-14T163231.507025.snakemake.log
new file mode 100644
index 0000000..7759d1b
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163231.507025.snakemake.log
@@ -0,0 +1,11 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 96:
+Error:
+  NameError: name 'snakemake' is not defined
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 104, in <lambda>
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/snakemake.py", line 41, in format_input_templates_to_be_expanded
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/src/formatter.py", line 49, in format_input_templates_to_be_expanded (rule methods_M1_default_run, line 160, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163257.053515.snakemake.log b/.snakemake/log/2024-03-14T163257.053515.snakemake.log
new file mode 100644
index 0000000..087f13d
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163257.053515.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 106:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'output'
+Wildcards:
+  pre=out/data/D1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 66, in generate_input (rule process_P1_default_run, line 170, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163305.951491.snakemake.log b/.snakemake/log/2024-03-14T163305.951491.snakemake.log
new file mode 100644
index 0000000..7977cd1
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163305.951491.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 106:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'outputs'
+Wildcards:
+  pre=out/data/D2/default/process/P1/default
+  name=D2
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 66, in generate_input (rule methods_M2_default_run, line 170, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163320.420139.snakemake.log b/.snakemake/log/2024-03-14T163320.420139.snakemake.log
new file mode 100644
index 0000000..ecd71e2
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163320.420139.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 104:
+Error:
+  AttributeError: module 'snakemake' has no attribute 'outputs'
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 66, in generate_input (rule methods_M2_default_run, line 165, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163403.662029.snakemake.log b/.snakemake/log/2024-03-14T163403.662029.snakemake.log
new file mode 100644
index 0000000..436f025
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163403.662029.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 104:
+Error:
+  NameError: name 'output' is not defined
+Wildcards:
+  pre=out/data/D1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 66, in generate_input (rule process_P1_default_run, line 165, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163411.484644.snakemake.log b/.snakemake/log/2024-03-14T163411.484644.snakemake.log
new file mode 100644
index 0000000..f35e5b2
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163411.484644.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 104:
+Error:
+  NameError: name 'outputs' is not defined
+Wildcards:
+  pre=out/data/D1/default/process/P2/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 66, in generate_input (rule methods_M2_default_run, line 165, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-14T163451.343675.snakemake.log b/.snakemake/log/2024-03-14T163451.343675.snakemake.log
new file mode 100644
index 0000000..5471387
--- /dev/null
+++ b/.snakemake/log/2024-03-14T163451.343675.snakemake.log
@@ -0,0 +1,9 @@
+Building DAG of jobs...
+InputFunctionException in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 106:
+Error:
+  TypeError: 'module' object is not iterable
+Wildcards:
+  pre=out/data/D1/default/process/P1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 70, in generate_input (rule methods_M1_default_run, line 167, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-15T122916.746366.snakemake.log b/.snakemake/log/2024-03-15T122916.746366.snakemake.log
new file mode 100644
index 0000000..261c9fb
--- /dev/null
+++ b/.snakemake/log/2024-03-15T122916.746366.snakemake.log
@@ -0,0 +1,11 @@
+Building DAG of jobs...
+InputFunctionException in rule process_P2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Error:
+  NameError: name 'snakemake' is not defined
+Wildcards:
+  pre=out/data/D1/default
+  name=D1
+Traceback:
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/Snakefile", line 103, in <lambda>
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/snakemake.py", line 41, in format_input_templates_to_be_expanded
+  File "/home/dani/Documents/omnibenchmark/omni_workflow/src/formatter.py", line 49, in format_input_templates_to_be_expanded (rule process_P2_default_run, line 156, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
diff --git a/.snakemake/log/2024-03-15T122928.437240.snakemake.log b/.snakemake/log/2024-03-15T122928.437240.snakemake.log
new file mode 100644
index 0000000..cf351c8
--- /dev/null
+++ b/.snakemake/log/2024-03-15T122928.437240.snakemake.log
@@ -0,0 +1,267 @@
+Building DAG of jobs...
+Using shell: /usr/bin/bash
+Provided cores: 1 (use --cores to define parallelism)
+Rules claiming more threads will be scaled down.
+Job stats:
+job                       count
+----------------------  -------
+all                           1
+data_D1_default_run           1
+data_D2_default_run           1
+methods_M1_default_run        4
+methods_M2_default_run        4
+process_P1_default_run        2
+process_P2_default_run        2
+start_benchmark               1
+total                        16
+
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule start_benchmark:
+    output: log/system_profiling.txt
+    jobid: 2
+    reason: Missing output files: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+
+        echo '---------------' > log/system_profiling.txt
+        echo 'DATE' >> log/system_profiling.txt
+        date >> log/system_profiling.txt
+        echo '
+OS' >> log/system_profiling.txt
+        uname -a >> log/system_profiling.txt
+        echo '
+nproc' >> log/system_profiling.txt
+        nproc >> log/system_profiling.txt
+        echo '
+cgroups' >> log/system_profiling.txt
+        ## to detect docker runs
+        cat /proc/1/cgroup >> log/system_profiling.txt        
+        
+[Fri Mar 15 12:29:28 2024]
+Finished job 2.
+1 of 16 steps (6%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule data_D2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt
+    jobid: 12
+    reason: Missing output files: out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 12.
+2 of 16 steps (12%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
+    jobid: 8
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 8.
+3 of 16 steps (19%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/D1.txt.gz
+    jobid: 4
+    reason: Missing output files: out/data/D1/default/process/P1/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 4.
+4 of 16 steps (25%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 15
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 15.
+5 of 16 steps (31%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
+    jobid: 7
+    reason: Missing output files: out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 7.
+6 of 16 steps (38%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule process_P1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/D2.txt.gz
+    jobid: 5
+    reason: Missing output files: out/data/D2/default/process/P1/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:28 2024]
+Finished job 5.
+7 of 16 steps (44%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:28 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
+    jobid: 11
+    reason: Missing output files: out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P2/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 11.
+8 of 16 steps (50%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
+    jobid: 3
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 3.
+9 of 16 steps (56%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
+    jobid: 13
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 13.
+10 of 16 steps (62%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P2/default/D1.txt.gz
+    jobid: 1
+    reason: Missing output files: out/data/D1/default/process/P2/default/D1.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 1.
+11 of 16 steps (69%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule process_P2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P2/default/D2.txt.gz
+    jobid: 14
+    reason: Missing output files: out/data/D2/default/process/P2/default/D2.txt.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 14.
+12 of 16 steps (75%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule methods_M1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
+    jobid: 6
+    reason: Missing output files: out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D2/default/process/P1/default, name=D2
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 6.
+13 of 16 steps (81%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule data_D1_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/D1_params.txt
+    jobid: 9
+    reason: Missing output files: out/data/D1/default/D1.txt.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json; Input files updated by another job: log/system_profiling.txt
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 9.
+14 of 16 steps (88%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule methods_M2_default_run:
+    input: log/system_profiling.txt
+    output: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
+    jobid: 10
+    reason: Missing output files: out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz; Input files updated by another job: log/system_profiling.txt
+    wildcards: pre=out/data/D1/default/process/P1/default, name=D1
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 10.
+15 of 16 steps (94%) done
+Select jobs to execute...
+Execute 1 jobs...
+
+[Fri Mar 15 12:29:29 2024]
+localrule all:
+    input: out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/D2_params.txt, out/data/D2/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D2/default/process/P2/default/D2.txt.gz, out/data/D1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
+    jobid: 0
+    reason: Input files updated by another job: out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/process/P1/default/D1.txt.gz, out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/D1.meta.json, out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz, out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz, out/data/D1/default/D1.txt.gz, out/data/D2/default/process/P1/default/D2.txt.gz, out/data/D2/default/D2.meta.json, out/data/D2/default/D2_params.txt, out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz, out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz, out/data/D1/default/D1_params.txt, out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz, out/data/D1/default/process/P2/default/D1.txt.gz, out/data/D2/default/D2.txt.gz, out/data/D2/default/process/P2/default/D2.txt.gz
+    resources: tmpdir=/tmp
+
+[Fri Mar 15 12:29:29 2024]
+Finished job 0.
+16 of 16 steps (100%) done
+Complete log: .snakemake/log/2024-03-15T122928.437240.snakemake.log
diff --git a/.snakemake/log/2024-03-15T123818.625046.snakemake.log b/.snakemake/log/2024-03-15T123818.625046.snakemake.log
new file mode 100644
index 0000000..b5eca96
--- /dev/null
+++ b/.snakemake/log/2024-03-15T123818.625046.snakemake.log
@@ -0,0 +1,13 @@
+Building DAG of jobs...
+AmbiguousRuleException:
+Rules process_P2_default_run and methods_M1_default_run are ambiguous for the file out/data/D2/default/process/P1/default/D2.txt.gz.
+Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
+Wildcards:
+	process_P2_default_run: module=D2/default/process/P1,name=D2,params=default,pre=out
+	methods_M1_default_run: module=D2/default/process/P1,name=D2,params=default,pre=out
+Expected input files:
+	process_P2_default_run: log/system_profiling.txt
+	methods_M1_default_run: log/system_profiling.txt
+Expected output files:
+	process_P2_default_run: out/data/D2/default/process/P1/default/D2.txt.gz
+	methods_M1_default_run: out/data/D2/default/process/P1/default/D2.txt.gz
diff --git a/.snakemake/log/2024-03-15T123849.977513.snakemake.log b/.snakemake/log/2024-03-15T123849.977513.snakemake.log
new file mode 100644
index 0000000..f98dcbb
--- /dev/null
+++ b/.snakemake/log/2024-03-15T123849.977513.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Wildcards in input files cannot be determined from output files: (rule methods_M2_default_run, line 156, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-15T124055.329280.snakemake.log b/.snakemake/log/2024-03-15T124055.329280.snakemake.log
new file mode 100644
index 0000000..0e81ab6
--- /dev/null
+++ b/.snakemake/log/2024-03-15T124055.329280.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule process_P1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Wildcards in input files cannot be determined from output files: (rule process_P1_default_run, line 156, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-15T124103.733980.snakemake.log b/.snakemake/log/2024-03-15T124103.733980.snakemake.log
new file mode 100644
index 0000000..f98dcbb
--- /dev/null
+++ b/.snakemake/log/2024-03-15T124103.733980.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M2_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Wildcards in input files cannot be determined from output files: (rule methods_M2_default_run, line 156, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/log/2024-03-15T124229.400538.snakemake.log b/.snakemake/log/2024-03-15T124229.400538.snakemake.log
new file mode 100644
index 0000000..abe8981
--- /dev/null
+++ b/.snakemake/log/2024-03-15T124229.400538.snakemake.log
@@ -0,0 +1,4 @@
+Building DAG of jobs...
+WildcardError in rule methods_M1_default_run in file /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile, line 95:
+Wildcards in input files cannot be determined from output files: (rule methods_M1_default_run, line 156, /home/dani/Documents/omnibenchmark/omni_workflow/Snakefile)
+'module'
diff --git a/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLm1ldGEuanNvbg== b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLm1ldGEuanNvbg==
new file mode 100644
index 0000000..fe464f2
--- /dev/null
+++ b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLm1ldGEuanNvbg==
@@ -0,0 +1 @@
+{"code": "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", "rule": "D1_materialize", "input": ["log/system_profiling.txt"], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710332036.909213, "endtime": 1710332036.9852142, "job_hash": 8310041450412, "conda_env": null, "container_img_url": null, "input_checksums": {"log/system_profiling.txt": "152b0c9428d0bed1ecaf85f0bd11ed6c0794bafa815e6c9480fce1a60fb7a9f7"}}
\ No newline at end of file
diff --git a/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLnR4dC5neg== b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLnR4dC5neg==
new file mode 100644
index 0000000..fe464f2
--- /dev/null
+++ b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxLnR4dC5neg==
@@ -0,0 +1 @@
+{"code": "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", "rule": "D1_materialize", "input": ["log/system_profiling.txt"], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710332036.909213, "endtime": 1710332036.9852142, "job_hash": 8310041450412, "conda_env": null, "container_img_url": null, "input_checksums": {"log/system_profiling.txt": "152b0c9428d0bed1ecaf85f0bd11ed6c0794bafa815e6c9480fce1a60fb7a9f7"}}
\ No newline at end of file
diff --git a/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxX3BhcmFtcy50eHQ= b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxX3BhcmFtcy50eHQ=
new file mode 100644
index 0000000..4995943
--- /dev/null
+++ b/.snakemake/metadata/ZGF0YS9EMS9kZWZhdWx0L0QxX3BhcmFtcy50eHQ=
@@ -0,0 +1 @@
+{"code": "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", "rule": "D1_materialize", "input": ["log/system_profiling.txt"], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710332036.913213, "endtime": 1710332036.9852142, "job_hash": 8310041450412, "conda_env": null, "container_img_url": null, "input_checksums": {"log/system_profiling.txt": "152b0c9428d0bed1ecaf85f0bd11ed6c0794bafa815e6c9480fce1a60fb7a9f7"}}
\ No newline at end of file
diff --git a/.snakemake/metadata/ZGF0YS9EMi9kZWZhdWx0L0QyLm1ldGEuanNvbg== b/.snakemake/metadata/ZGF0YS9EMi9kZWZhdWx0L0QyLm1ldGEuanNvbg==
new file mode 100644
index 0000000..79ec4cd
--- /dev/null
+++ b/.snakemake/metadata/ZGF0YS9EMi9kZWZhdWx0L0QyLm1ldGEuanNvbg==
@@ -0,0 +1 @@
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+{"code": "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", "rule": "methods_M2_-d1__-e_2_run", "input": [], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710419742.232773, "endtime": 1710419742.3047738, "job_hash": 8288440430784, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9EMi50eHQuZ3o= b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9EMi50eHQuZ3o=
new file mode 100644
index 0000000..36528c2
--- /dev/null
+++ b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9EMi50eHQuZ3o=
@@ -0,0 +1 @@
+{"code": "gASVKAIAAAAAAAAoQ4CXAHQBAAAAAAAAAAAAAHQDAAAAAAAAAAAAAGoCAAAAAAAAAABkAWQCpgIAAKsCAAAAAAAAAAB8FXwAfAF8AnwDfAR8BXwGdAYAAAAAAAAAAAAAfAd8CHwUfAl8CnwMfA18DnwQfBF8EnwWfBemFwAAqxcAAAAAAAAAAAEAZABTAJQojAVpbnB1dJSMBm91dHB1dJSMBnBhcmFtc5SMCXdpbGRjYXJkc5SMB3RocmVhZHOUjAlyZXNvdXJjZXOUjANsb2eUjARydWxllIwJY29uZGFfZW52lIwNY29udGFpbmVyX2ltZ5SMEHNpbmd1bGFyaXR5X2FyZ3OUjA91c2Vfc2luZ3VsYXJpdHmUjAtlbnZfbW9kdWxlc5SMDGJlbmNoX3JlY29yZJSMBWpvYmlklIwIaXNfc2hlbGyUjA9iZW5jaF9pdGVyYXRpb26UjA9jbGVhbnVwX3NjcmlwdHOUjApzaGFkb3dfZGlylIwNZWRpdF9ub3RlYm9va5SMD2NvbmRhX2Jhc2VfcGF0aJSMB2Jhc2VkaXKUjBBzb3VyY2VjYWNoZV9wYXRolIwYcnVudGltZV9zb3VyY2VjYWNoZV9wYXRolIwYX19pc19zbmFrZW1ha2VfcnVsZV9mdW5jlHSUXZQoTowDc3JjlIwPZG9fc29tZXRoaW5nLnB5lGUojAZzY3JpcHSUjAJvcJSMBGpvaW6UjAZjb25maWeUdJR0lC4=", "rule": "process_P2_-a_1__-c_0_1_run", "input": [], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710419741.3527641, "endtime": 1710419741.4247649, "job_hash": 8288440424844, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00xL2RlZmF1bHQvRDIubW9kZWwub3V0Lmd6 b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00xL2RlZmF1bHQvRDIubW9kZWwub3V0Lmd6
new file mode 100644
index 0000000..b47baa6
--- /dev/null
+++ b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00xL2RlZmF1bHQvRDIubW9kZWwub3V0Lmd6
@@ -0,0 +1 @@
+{"code": "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", "rule": "methods_M1_default_run", "input": [], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710419741.2807634, "endtime": 1710419741.3527641, "job_hash": 8288440423820, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMS9EMi5tb2RlbC5vdXQuZ3o= b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMS9EMi5tb2RlbC5vdXQuZ3o=
new file mode 100644
index 0000000..e67278d
--- /dev/null
+++ b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMS9EMi5tb2RlbC5vdXQuZ3o=
@@ -0,0 +1 @@
+{"code": "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", "rule": "methods_M2_-d1__-e_1_run", "input": [], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710419741.5007656, "endtime": 1710419741.5727663, "job_hash": 8288440431396, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMi9EMi5tb2RlbC5vdXQuZ3o= b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMi9EMi5tb2RlbC5vdXQuZ3o=
new file mode 100644
index 0000000..2b62d6e
--- /dev/null
+++ b/.snakemake/metadata/b3V0L2RhdGEvRDIvZGVmYXVsdC9wcm9jZXNzL1AyLy1hXzFfXy1jXzBfMS9tZXRob2RzL00yLy1kMV9fLWVfMi9EMi5tb2RlbC5vdXQuZ3o=
@@ -0,0 +1 @@
+{"code": "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", "rule": "methods_M2_-d1__-e_2_run", "input": [], "log": [], "params": [], "shellcmd": null, "incomplete": false, "starttime": 1710419742.0887716, "endtime": 1710419742.1607723, "job_hash": 8288440423616, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMS50eHQ= b/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMS50eHQ=
new file mode 100644
index 0000000..149a6e2
--- /dev/null
+++ b/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMS50eHQ=
@@ -0,0 +1 @@
+{"code": "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", "rule": "wildcard_awareness", "input": ["data/D1/default/D1.meta.json", "data/D1/default/D1.txt.gz", "data/D1/default/D1_params.txt", "data/D2/default/D2.meta.json", "data/D2/default/D2.txt.gz", "data/D2/default/D2_params.txt"], "log": [], "params": [], "shellcmd": "\n        echo id=D1,params=default,stage=data > log/data_default_D1.txt\n        ", "incomplete": false, "starttime": 1710164909.8073618, "endtime": 1710164909.8073618, "job_hash": 8597265472088, "conda_env": null, "container_img_url": null, "input_checksums": {"data/D1/default/D1.txt.gz": "0f360baa9451181cd0144cecedb4573842f535649b1839adbcfcf4679713c42e", "data/D1/default/D1.meta.json": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D1/default/D1_params.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D2/default/D2.txt.gz": "0f360baa9451181cd0144cecedb4573842f535649b1839adbcfcf4679713c42e", "data/D2/default/D2.meta.json": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D2/default/D2_params.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}}
\ No newline at end of file
diff --git a/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMi50eHQ= b/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMi50eHQ=
new file mode 100644
index 0000000..d7fd9db
--- /dev/null
+++ b/.snakemake/metadata/bG9nL2RhdGFfZGVmYXVsdF9EMi50eHQ=
@@ -0,0 +1 @@
+{"code": "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", "rule": "wildcard_awareness", "input": ["data/D1/default/D1.meta.json", "data/D1/default/D1.txt.gz", "data/D1/default/D1_params.txt", "data/D2/default/D2.meta.json", "data/D2/default/D2.txt.gz", "data/D2/default/D2_params.txt"], "log": [], "params": [], "shellcmd": "\n        echo id=D2,params=default,stage=data > log/data_default_D2.txt\n        ", "incomplete": false, "starttime": 1710164909.8113618, "endtime": 1710164909.8113618, "job_hash": 8597265479872, "conda_env": null, "container_img_url": null, "input_checksums": {"data/D1/default/D1.txt.gz": "0f360baa9451181cd0144cecedb4573842f535649b1839adbcfcf4679713c42e", "data/D1/default/D1.meta.json": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D1/default/D1_params.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D2/default/D2.txt.gz": "0f360baa9451181cd0144cecedb4573842f535649b1839adbcfcf4679713c42e", "data/D2/default/D2.meta.json": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b", "data/D2/default/D2_params.txt": "01ba4719c80b6fe911b091a7c05124b64eeece964e09c058ef8f9805daca546b"}}
\ No newline at end of file
diff --git a/.snakemake/metadata/bG9nL3N5c3RlbV9wcm9maWxpbmcudHh0 b/.snakemake/metadata/bG9nL3N5c3RlbV9wcm9maWxpbmcudHh0
new file mode 100644
index 0000000..608dd8f
--- /dev/null
+++ b/.snakemake/metadata/bG9nL3N5c3RlbV9wcm9maWxpbmcudHh0
@@ -0,0 +1 @@
+{"code": "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", "rule": "start_benchmark", "input": [], "log": [], "params": [], "shellcmd": "\n        echo '---------------' > log/system_profiling.txt\n        echo 'DATE' >> log/system_profiling.txt\n        date >> log/system_profiling.txt\n        echo '\nOS' >> log/system_profiling.txt\n        uname -a >> log/system_profiling.txt\n        echo '\nnproc' >> log/system_profiling.txt\n        nproc >> log/system_profiling.txt\n        echo '\ncgroups' >> log/system_profiling.txt\n        ## to detect docker runs\n        cat /proc/1/cgroup >> log/system_profiling.txt        \n        ", "incomplete": false, "starttime": 1710502168.4593375, "endtime": 1710502168.4633374, "job_hash": 8315343961450, "conda_env": null, "container_img_url": null, "input_checksums": {}}
\ No newline at end of file
diff --git a/Pipfile b/Pipfile
index c51d783..4e3b61e 100644
--- a/Pipfile
+++ b/Pipfile
@@ -5,11 +5,12 @@ name = "pypi"
 
 [packages]
 snakemake = "==8.4.3"
-networkx = "*"
-matplotlib = "*"
+networkx = "~=3.2.1"
+matplotlib = "~=3.8.3"
 omni-schema = "==0.0.1"
 linkml-runtime = ">=1.7.0"
 rdflib = "==7.0.0"
+pyyaml = "~=6.0.1"
 
 [dev-packages]
 
diff --git a/Pipfile.lock b/Pipfile.lock
new file mode 100644
index 0000000..7e5b2b0
--- /dev/null
+++ b/Pipfile.lock
@@ -0,0 +1,1474 @@
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+                "sha256:44a2754372e32ab315734c6c73b24351d06e77ffff6ae27d2ecf14cf3d229202",
+                "sha256:490b0ee15c1a55be9c1bd8609b8cecd60e325f0575fc98f50058eae366e01f41",
+                "sha256:49aac49dc4782cb04f58986e81ea0b4768e4ff197b57324dcbd7699c5dfb40b9",
+                "sha256:5eb404d89131ec9b4f748fa5cfb5346802e5ee8836f57d516576e61f304f3b7b",
+                "sha256:5f15814a33e42b04e3de432e573aa557f9f0f56458745c2074952f564c50e664",
+                "sha256:5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d",
+                "sha256:66027d667efe95cc4fa945af59f92c5a02c6f5bb6012bff9e60542c74c75c362",
+                "sha256:66dfbaa7cfa3eb707bbfcd46dab2bc6207b005cbc9caa2199bcbc81d95071a00",
+                "sha256:685f568fa5e627e93f3b52fda002c7ed2fa1800b50ce51f6ed1d572d8ab3e7fc",
+                "sha256:6906c4100a8fcbf2fa735f6059214bb13b97f75b1a61777fcf6432121ef12ef1",
+                "sha256:6a42cd0cfa8ffc1915aef79cb4284f6383d8a3e9dcca70c445dcfdd639d51267",
+                "sha256:6dcfcffe73710be01d90cae08c3e548d90932d37b39ef83969ae135d36ef3956",
+                "sha256:6f6eac2360f2d543cc875a0e5efd413b6cbd483cb3ad7ebf888884a6e0d2e966",
+                "sha256:72554a23c78a8e7aa02abbd699d129eead8b147a23c56e08d08dfc29cfdddca1",
+                "sha256:73870c364c11f03ed072dda68ff7aea6d2a3a5c3fe250d917a429c7432e15228",
+                "sha256:73aa7d98215d39b8455f103de64391cb79dfcad601701a3aa0dddacf74911d72",
+                "sha256:75ea7d0ee2a15733684badb16de6794894ed9c55aa5e9903260922f0482e687d",
+                "sha256:7bd2d7ff69a2cac767fbf7a2b206add2e9a210e57947dd7ce03e25d03d2de292",
+                "sha256:807cc8543a477ab7422f1120a217054f958a66ef7314f76dd9e77d3f02cdccd0",
+                "sha256:8e9723528b9f787dc59168369e42ae1c3b0d3fadb2f1a71de14531d321ee05b0",
+                "sha256:9090c9e676d5236a6948330e83cb89969f433b1943a558968f659ead07cb3b36",
+                "sha256:9153ed35fc5e4fa3b2fe97bddaa7cbec0ed22412b85bcdaf54aeba92ea37428c",
+                "sha256:9159485323798c8dc530a224bd3ffcf76659319ccc7bbd52e01e73bd0241a0c5",
+                "sha256:941988b89b4fd6b41c3f0bfb20e92bd23746579736b7343283297c4c8cbae68f",
+                "sha256:94265b00870aa407bd0cbcfd536f17ecde43b94fb8d228560a1e9d3041462d73",
+                "sha256:98b5e1f498a8ca1858a1cdbffb023bfd954da4e3fa2c0cb5853d40014557248b",
+                "sha256:9b201ae332c3637a42f02d1045e1d0cccfdc41f1f2f801dafbaa7e9b4797bfc2",
+                "sha256:a0ea261ce52b5952bf669684a251a66df239ec6d441ccb59ec7afa882265d593",
+                "sha256:a33a747400b94b6d6b8a165e4480264a64a78c8a4c734b62136062e9a248dd39",
+                "sha256:a452f9ca3e3267cd4d0fcf2edd0d035b1934ac2bd7e0e57ac91ad6b95c0c6389",
+                "sha256:a86373cf37cd7764f2201b76496aba58a52e76dedfaa698ef9e9688bfd9e41cf",
+                "sha256:ac83a914ebaf589b69f7d0a1277602ff494e21f4c2f743313414378f8f50a4cf",
+                "sha256:aefbc4cb0a54f91af643660a0a150ce2c090d3652cf4052a5397fb2de549cd89",
+                "sha256:b3646eefa23daeba62643a58aac816945cadc0afaf21800a1421eeba5f6cfb9c",
+                "sha256:b47cfad9e9bbbed2339081f4e346c93ecd7ab504299403320bf85f7f85c7d46c",
+                "sha256:b935ae30c6e7400022b50f8d359c03ed233d45b725cfdd299462f41ee5ffba6f",
+                "sha256:bb2dee3874a500de01c93d5c71415fcaef1d858370d405824783e7a8ef5db440",
+                "sha256:bc57efac2da352a51cc4658878a68d2b1b67dbe9d33c36cb826ca449d80a8465",
+                "sha256:bf5703fdeb350e36885f2875d853ce13172ae281c56e509f4e6eca049bdfb136",
+                "sha256:c31f72b1b6624c9d863fc095da460802f43a7c6868c5dda140f51da24fd47d7b",
+                "sha256:c5cd603b575ebceca7da5a3a251e69561bec509e0b46e4993e1cac402b7247b8",
+                "sha256:d2efee35b4b0a347e0d99d28e884dfd82797852d62fcd7ebdeee26f3ceb72cf3",
+                "sha256:d462f28826f4657968ae51d2181a074dfe03c200d6131690b7d65d55b0f360f8",
+                "sha256:d5e49454f19ef621089e204f862388d29e6e8d8b162efce05208913dde5b9ad6",
+                "sha256:da4813f751142436b075ed7aa012a8778aa43a99f7b36afe9b742d3ed8bdc95e",
+                "sha256:db2e408d983b0e61e238cf579c09ef7020560441906ca990fe8412153e3b291f",
+                "sha256:db98ad84a55eb09b3c32a96c576476777e87c520a34e2519d3e59c44710c002c",
+                "sha256:dbed418ba5c3dce92619656802cc5355cb679e58d0d89b50f116e4a9d5a9603e",
+                "sha256:dcdba5c86e368442528f7060039eda390cc4091bfd1dca41e8046af7c910dda8",
+                "sha256:decbfa2f618fa8ed81c95ee18a387ff973143c656ef800c9f24fb7e9c16054e2",
+                "sha256:e4fdb9275308292e880dcbeb12546df7f3e0f96c6b41197e0cf37d2826359020",
+                "sha256:eb1b046be06b0fce7249f1d025cd359b4b80fc1c3e24ad9eca33e0dcdb2e4a35",
+                "sha256:eb6e651000a19c96f452c85132811d25e9264d836951022d6e81df2fff38337d",
+                "sha256:ed867c42c268f876097248e05b6117a65bcd1e63b779e916fe2e33cd6fd0d3c3",
+                "sha256:edfad1d29c73f9b863ebe7082ae9321374ccb10879eeabc84ba3b69f2579d537",
+                "sha256:f2058f813d4f2b5e3a9eb2eb3faf8f1d99b81c3e51aeda4b168406443e8ba809",
+                "sha256:f6b2d0c6703c988d334f297aa5df18c45e97b0af3679bb75059e0e0bd8b1069d",
+                "sha256:f8212564d49c50eb4565e502814f694e240c55551a5f1bc841d4fcaabb0a9b8a",
+                "sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==1.16.0"
+        },
+        "yte": {
+            "hashes": [
+                "sha256:14ccfcb57d60b7652041b606129851423805140b22f52f5152f7c2692cd7b905",
+                "sha256:d2d77e53eafca74f58234fcd3fea28cc0a719e4f3784911511e35e86594bc880"
+            ],
+            "markers": "python_version >= '3.7'",
+            "version": "==1.5.4"
+        }
+    },
+    "develop": {}
+}
diff --git a/Snakefile b/Snakefile
index bf2c69a..2cc3e2b 100644
--- a/Snakefile
+++ b/Snakefile
@@ -15,9 +15,8 @@ include: 'snakemake.py'
 configfile: op.join('data', 'Benchmark_001.yaml')
 
 rule all:
-    input:
-        expand(all_paths)
-               
+    input: expand(all_paths)
+
 
 rule start_benchmark:
     output:
@@ -63,6 +62,7 @@ rule start_benchmark:
 #         script:
 #             op.join('src', 'do_something.py')
 
+
 stages = converter.get_benchmark_stages()
 for node in G.nodes:
     stage_id = node.stage_id
@@ -70,6 +70,7 @@ for node in G.nodes:
     param_id = node.param_id
 
     stage = stages[stage_id]
+
     if converter.is_initial(stage):
         rule:
             name: f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
@@ -95,9 +96,13 @@ for node in G.nodes:
             wildcard_constraints:
                 #pre = '(.*\/.*)+',
                 stage='|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
-                # params = "default",
+                params = ".*",
+                module = '.*',
                 name='|'.join([re.escape(x) for x in converter.get_initial_datasets()])
             name:  f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
+            input:
+                lambda wildcards: format_input_templates_to_be_expanded(all_paths, wildcards, stage_id, module_id, param_id)
+                #'{pre}/data/{module}/{params}/{name}.txt.gz'
             output:
                 format_output_templates_to_be_expanded(stage_id=stage_id, module_id=module_id, param_id=param_id)
                 # "{pre}/{stage}/{dataset}/{params}/{dataset}_params.txt"
diff --git a/log/system_profiling.txt b/log/system_profiling.txt
new file mode 100644
index 0000000..7e0e2d4
--- /dev/null
+++ b/log/system_profiling.txt
@@ -0,0 +1,12 @@
+---------------
+DATE
+Fr 15 Mär 2024 12:29:28 CET
+
+OS
+Linux dani-ZenBook 6.5.0-25-generic #25~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 20 16:09:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
+
+nproc
+1
+
+cgroups
+0::/init.scope
diff --git a/main.py b/main.py
index 888d281..f6aa112 100644
--- a/main.py
+++ b/main.py
@@ -29,10 +29,6 @@
             print('    Params:', converter.get_module_parameters(module))
         print('------')
 
-    for dataset in converter.get_initial_datasets():
-        result = fmt.format_dataset_templates_to_be_expanded(converter, dataset)
-        print(result)
-
     print('------')
     stages = converter.get_benchmark_stages()
     for stage_id in stages:
@@ -57,7 +53,4 @@
                 paths = construct_output_paths(converter, prefix='out', nodes=path)
                 all_paths.update(paths)
 
-    all_paths = list(all_paths)
-
-    print([re.match(r'out/data/([^/]+)/', x).group(1) for x in all_paths])
-
+    all_paths = list(all_paths)
\ No newline at end of file
diff --git a/out/data/D1/default/D1.meta.json b/out/data/D1/default/D1.meta.json
new file mode 100644
index 0000000..7e1bf57
--- /dev/null
+++ b/out/data/D1/default/D1.meta.json
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/D1.meta.json using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/D1.txt.gz b/out/data/D1/default/D1.txt.gz
new file mode 100644
index 0000000..55bcd6a
--- /dev/null
+++ b/out/data/D1/default/D1.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/D1.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/D1_params.txt b/out/data/D1/default/D1_params.txt
new file mode 100644
index 0000000..3602535
--- /dev/null
+++ b/out/data/D1/default/D1_params.txt
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/D1_params.txt using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P1/default/D1.txt.gz b/out/data/D1/default/process/P1/default/D1.txt.gz
new file mode 100644
index 0000000..0755b28
--- /dev/null
+++ b/out/data/D1/default/process/P1/default/D1.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P1/default/D1.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default D1
+  rule is process_P1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz b/out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
new file mode 100644
index 0000000..1df58d7
--- /dev/null
+++ b/out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P1/default/methods/M1/default/D1.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default/process/P1/default D1
+  rule is methods_M1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz b/out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
new file mode 100644
index 0000000..e202f9b
--- /dev/null
+++ b/out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P1/default/methods/M2/default/D1.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default/process/P1/default D1
+  rule is methods_M2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P2/default/D1.txt.gz b/out/data/D1/default/process/P2/default/D1.txt.gz
new file mode 100644
index 0000000..b595b28
--- /dev/null
+++ b/out/data/D1/default/process/P2/default/D1.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P2/default/D1.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default D1
+  rule is process_P2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz b/out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
new file mode 100644
index 0000000..26baf35
--- /dev/null
+++ b/out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P2/default/methods/M1/default/D1.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default/process/P2/default D1
+  rule is methods_M1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz b/out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
new file mode 100644
index 0000000..454a020
--- /dev/null
+++ b/out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D1/default/process/P2/default D1
+  rule is methods_M2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/D2.meta.json b/out/data/D2/default/D2.meta.json
new file mode 100644
index 0000000..29e43ed
--- /dev/null
+++ b/out/data/D2/default/D2.meta.json
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/D2.meta.json using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/D2.txt.gz b/out/data/D2/default/D2.txt.gz
new file mode 100644
index 0000000..bc5ca2b
--- /dev/null
+++ b/out/data/D2/default/D2.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/D2.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/D2_params.txt b/out/data/D2/default/D2_params.txt
new file mode 100644
index 0000000..b562bc5
--- /dev/null
+++ b/out/data/D2/default/D2_params.txt
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/D2_params.txt using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are 
+  rule is data_D2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P1/default/D2.txt.gz b/out/data/D2/default/process/P1/default/D2.txt.gz
new file mode 100644
index 0000000..187f888
--- /dev/null
+++ b/out/data/D2/default/process/P1/default/D2.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P1/default/D2.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default D2
+  rule is process_P1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz b/out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
new file mode 100644
index 0000000..bb898e2
--- /dev/null
+++ b/out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P1/default/methods/M1/default/D2.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default/process/P1/default D2
+  rule is methods_M1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz b/out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
new file mode 100644
index 0000000..9f42dd0
--- /dev/null
+++ b/out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P1/default/methods/M2/default/D2.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default/process/P1/default D2
+  rule is methods_M2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P2/default/D2.txt.gz b/out/data/D2/default/process/P2/default/D2.txt.gz
new file mode 100644
index 0000000..091734e
--- /dev/null
+++ b/out/data/D2/default/process/P2/default/D2.txt.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P2/default/D2.txt.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default D2
+  rule is process_P2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz b/out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
new file mode 100644
index 0000000..4ea04e2
--- /dev/null
+++ b/out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P2/default/methods/M1/default/D2.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default/process/P2/default D2
+  rule is methods_M1_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz b/out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
new file mode 100644
index 0000000..11e12d9
--- /dev/null
+++ b/out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz
@@ -0,0 +1,7 @@
+Processed log/system_profiling.txt to out/data/D2/default/process/P2/default/methods/M2/default/D2.model.out.gz using params  and threads 1
+  bench_iteration is None
+  resources are 1 1 /tmp
+  wildcards are out/data/D2/default/process/P2/default D2
+  rule is methods_M2_default_run
+  scriptdir is /home/dani/Documents/omnibenchmark/omni_workflow/src
+  params are 
diff --git a/output_dag.png b/output_dag.png
new file mode 100644
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diff --git a/snakemake.py b/snakemake.py
index d4d31ba..bd87992 100644
--- a/snakemake.py
+++ b/snakemake.py
@@ -33,13 +33,9 @@ def format_name(path, prefix):
 all_paths = [format_name(path, prefix) for path in list(all_paths)]
 
 
-def format_dataset_templates_to_be_expanded(dataset):
-    return fmt.format_dataset_templates_to_be_expanded(converter, dataset)
-
-
 def format_output_templates_to_be_expanded(stage_id, module_id, param_id, name=None, initial=False):
     return fmt.format_output_templates_to_be_expanded(converter, stage_id, module_id, param_id, name, initial)
 
 
-def format_input_templates_to_be_expanded(stage_id, module_id):
-    return fmt.format_input_templates_to_be_expanded(converter, stage_id, module_id)
+def format_input_templates_to_be_expanded(all_paths, wildcards, stage_id, module_id, param_id):
+    return fmt.format_input_templates_to_be_expanded(converter, all_paths, wildcards, stage_id, module_id, param_id)
diff --git a/src/__pycache__/dag.cpython-311.pyc b/src/__pycache__/dag.cpython-311.pyc
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HcmV?d00001

diff --git a/src/converter/model_converter.py b/src/converter/model_converter.py
index 8daae70..5cc2ac6 100644
--- a/src/converter/model_converter.py
+++ b/src/converter/model_converter.py
@@ -20,8 +20,11 @@ def get_modules_by_stage(self, stage):
         return dict([(x.id, x) for x in stage.members])
 
     def get_stage_implicit_inputs(self, stage):
+        if isinstance(stage, str):
+            stage = self.get_benchmark_stages()[stage]
+
         if stage.initial:
-            return None
+            return []
 
         return [input.entries for input in stage.inputs]
 
@@ -30,9 +33,18 @@ def get_stage_explicit_inputs(self, stage):
         explicit = implicit
         if implicit is not None:
             all_stages = self.get_benchmark_stages()
-            all_stages_outputs = [self.get_stage_outputs(stage=stage_id) for stage_id in all_stages]
-            all_stages_outputs = merge_dict_list(all_stages_outputs)
+            all_stages_outputs = []
+            for stage_id in all_stages:
+                outputs = self.get_stage_outputs(stage=stage_id)
+                outputs = {
+                    key: value.format(input_dirname='{input_dirname}',
+                                      stage=stage_id,
+                                      module='{module}',
+                                      params='{params}',
+                                      name='{name}') for key, value in outputs.items()}
+                all_stages_outputs.append(outputs)
 
+            all_stages_outputs = merge_dict_list(all_stages_outputs)
             for i in range(len(implicit)):
                 explicit[i] = {key: None for key in implicit[i]}
 
@@ -42,6 +54,7 @@ def get_stage_explicit_inputs(self, stage):
 
                     explicit[i][in_deliverable] = curr_output
 
+        explicit = explicit[0] if len(explicit) > 0 else {}
         return explicit
 
     def get_stage_outputs(self, stage):
diff --git a/src/converter/yaml_converter.py b/src/converter/yaml_converter.py
index 4683e0f..1551254 100644
--- a/src/converter/yaml_converter.py
+++ b/src/converter/yaml_converter.py
@@ -44,6 +44,9 @@ def get_module_excludes(self, module):
         return excludes
 
     def get_stage_implicit_inputs(self, stage):
+        if isinstance(stage, str):
+            stage = self.get_benchmark_stages()[stage]
+
         if 'initial' in stage.keys() and stage['initial']:
             return None
 
diff --git a/src/dag.py b/src/dag.py
index 65735b6..39e8105 100644
--- a/src/dag.py
+++ b/src/dag.py
@@ -39,7 +39,7 @@ def expend_stage_nodes(converter, stage_id, stage):
         if not parameters or len(parameters) == 0:
             parameters = [['default']]
 
-        # parameters = [['default']]
+        parameters = [['default']]
         for param in parameters:
             node = Node(stage_id, module_id, param)
             nodes.append(node)
diff --git a/src/formatter.py b/src/formatter.py
index 33c098b..b1a945a 100644
--- a/src/formatter.py
+++ b/src/formatter.py
@@ -1,3 +1,4 @@
+import re
 
 ## f-strings: rule maker
 ## wildcards: output mapper (only params, currently)
@@ -39,8 +40,37 @@ def format_output_templates_to_be_expanded(converter, stage_id, module_id, param
                   params=param_id,
                   name=name) for x in converter.get_stage_outputs(stage_id).values()]
 
+    print(f'Output: {stage_id} {module_id} {param_id}: {o}')
     return o
 
 
-def format_input_templates_to_be_expanded(converter, stage_id, module_id, param_id):
-    return 'todo'
\ No newline at end of file
+def format_input_templates_to_be_expanded(converter, all_paths, wildcards, stage_id, module_id, param_id):
+    o = []
+
+    for x in converter.get_stage_explicit_inputs(stage_id).values():
+        prefix = wildcards.pre
+        name = wildcards.name
+
+        x = x.format(input_dirname='{pre}',
+                     stage='{stage}',
+                     module='{module}',
+                     params='{params}',
+                     name=name)
+
+        # Transform to regular expression pattern
+        #pattern = re.sub(r'\{pre\}', r'(.*)', x)
+        #pattern = re.sub(r'\{module\}', r'([^\/]+)', pattern)
+        #pattern = re.sub(r'\{params\}', r'([^\/]+)', pattern)
+
+        # Compile the pattern into a regular expression object
+        #regex = re.compile(pattern)
+
+        # Match file paths based on the pattern
+        #matched_files = [path for path in all_paths if regex.match(path) and (len(path) < len(prefix) or path.startswith(prefix))]
+        #o.extend(matched_files)
+
+
+
+    print(f'Pre: {wildcards}')
+    print(f'Input: {stage_id} {module_id} {param_id}: {o}')
+    return '{pre}/data/{module}/{params}/{name}.txt.gz'

From 7a6176002aa66210b31776b743e5d26d0128d425 Mon Sep 17 00:00:00 2001
From: Izaskun Mallona <izaskun.mallona@gmail.com>
Date: Fri, 15 Mar 2024 13:08:18 +0100
Subject: [PATCH 2/4] Generate only one preprocessed output

---
 Snakefile | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/Snakefile b/Snakefile
index 2cc3e2b..e192b5a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -15,7 +15,9 @@ include: 'snakemake.py'
 configfile: op.join('data', 'Benchmark_001.yaml')
 
 rule all:
-    input: expand(all_paths)
+    input:
+        #all_paths,
+        "out/data/D2/default/process/P1/default/D2.txt.gz"
 
 
 rule start_benchmark:
@@ -70,6 +72,7 @@ for node in G.nodes:
     param_id = node.param_id
 
     stage = stages[stage_id]
+    print('stage_id is', stage_id)
 
     if converter.is_initial(stage):
         rule:
@@ -95,17 +98,19 @@ for node in G.nodes:
         rule:
             wildcard_constraints:
                 #pre = '(.*\/.*)+',
-                stage='|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
-                params = ".*",
-                module = '.*',
+                stage= stage_id, # '|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
+                # params = ".*",
+                module = module_id,
                 name='|'.join([re.escape(x) for x in converter.get_initial_datasets()])
             name:  f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
             input:
-                lambda wildcards: format_input_templates_to_be_expanded(all_paths, wildcards, stage_id, module_id, param_id)
-                #'{pre}/data/{module}/{params}/{name}.txt.gz'
+                # lambda wildcards: format_input_templates_to_be_expanded(all_paths, wildcards, stage_id, module_id, param_id)
+                # format_input_templates_to_be_expanded()
+                '{pre}/{name}.txt.gz'
             output:
-                format_output_templates_to_be_expanded(stage_id=stage_id, module_id=module_id, param_id=param_id)
-                # "{pre}/{stage}/{dataset}/{params}/{dataset}_params.txt"
+                # format_output_templates_to_be_expanded(stage_id=stage_id, module_id=module_id, param_id=param_id)
+                "{pre}/{stage}/{module}/{params}/{name}.txt.gz"
+                # "out/data/D2/default/process/P1/default/D2.txt.gz"
             script:
                 op.join("src", "do_something.py")
 

From b693a8021e0b79747b223c65141744c6ad2a3f69 Mon Sep 17 00:00:00 2001
From: Izaskun Mallona <izaskun.mallona@gmail.com>
Date: Fri, 15 Mar 2024 13:47:46 +0100
Subject: [PATCH 3/4] Another incremental step (data -> pre)

---
 Snakefile | 34 +++++++++++++++-------------------
 1 file changed, 15 insertions(+), 19 deletions(-)

diff --git a/Snakefile b/Snakefile
index e192b5a..209d681 100644
--- a/Snakefile
+++ b/Snakefile
@@ -16,8 +16,10 @@ configfile: op.join('data', 'Benchmark_001.yaml')
 
 rule all:
     input:
-        #all_paths,
-        "out/data/D2/default/process/P1/default/D2.txt.gz"
+        # all_paths,
+        "out/data/D2/default/D2.dataext",
+        "out/data/D2/default/process/P1/default/D2.txt.gz",
+        # "out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz"
 
 
 rule start_benchmark:
@@ -67,26 +69,24 @@ rule start_benchmark:
 
 stages = converter.get_benchmark_stages()
 for node in G.nodes:
+    print('node is', node)
     stage_id = node.stage_id
     module_id = node.module_id
     param_id = node.param_id
 
     stage = stages[stage_id]
-    print('stage_id is', stage_id)
+    print('stage_id is', stage_id, 'and module_id is', module_id, 'is initial', converter.is_initial(stage))
 
     if converter.is_initial(stage):
         rule:
             name: f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
-            input:
-                op.join('log','system_profiling.txt')
             wildcard_constraints:
                 #pre = '(.*\/.*)+',
-                stage='|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
-                # params = "default",
-                name='|'.join([re.escape(x) for x in converter.get_initial_datasets()])
+                stage= 'data', #'|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
+                param = "default",
+                name= module_id # '|'.join([re.escape(x) for x in converter.get_initial_datasets()])
             output:
-                format_output_templates_to_be_expanded(stage_id=stage_id, module_id=module_id, param_id=param_id, name=module_id, initial=True)
-                # "out/data/{dataset}/{params}/{dataset}_params.txt"
+                "out/{stage}/{name}/{param}/{name}.dataext"
             script:
                 op.join('src','do_something.py')
     elif converter.is_terminal(stage):
@@ -97,20 +97,16 @@ for node in G.nodes:
     else:
         rule:
             wildcard_constraints:
-                #pre = '(.*\/.*)+',
+                #pre = '(.*\/.*)+' <- we should fstring pre here using the parent's path
                 stage= stage_id, # '|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
-                # params = ".*",
                 module = module_id,
-                name='|'.join([re.escape(x) for x in converter.get_initial_datasets()])
+                name='|'.join([re.escape(x) for x in converter.get_initial_datasets()]),
+                ext=".*$"
             name:  f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
             input:
-                # lambda wildcards: format_input_templates_to_be_expanded(all_paths, wildcards, stage_id, module_id, param_id)
-                # format_input_templates_to_be_expanded()
-                '{pre}/{name}.txt.gz'
+                '{pre}/{name}.dataext'
             output:
-                # format_output_templates_to_be_expanded(stage_id=stage_id, module_id=module_id, param_id=param_id)
-                "{pre}/{stage}/{module}/{params}/{name}.txt.gz"
-                # "out/data/D2/default/process/P1/default/D2.txt.gz"
+                "{pre}/{stage}/{module}/{params}/{name}.{ext}"
             script:
                 op.join("src", "do_something.py")
 

From 9aae950c2a5deedd25739c5625a7237d5129cad1 Mon Sep 17 00:00:00 2001
From: Izaskun Mallona <izaskun.mallona@gmail.com>
Date: Fri, 15 Mar 2024 13:59:42 +0100
Subject: [PATCH 4/4] Nested rule maker release candidate

---
 Snakefile | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/Snakefile b/Snakefile
index 209d681..9786ac5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -16,9 +16,9 @@ configfile: op.join('data', 'Benchmark_001.yaml')
 
 rule all:
     input:
-        # all_paths,
-        "out/data/D2/default/D2.dataext",
-        "out/data/D2/default/process/P1/default/D2.txt.gz",
+        all_paths,
+        # "out/data/D2/default/D2.dataext",
+        # "out/data/D2/default/process/P1/default/D2.txt.gz",
         # "out/data/D1/default/process/P2/default/methods/M2/default/D1.model.out.gz"
 
 
@@ -81,12 +81,13 @@ for node in G.nodes:
         rule:
             name: f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
             wildcard_constraints:
-                #pre = '(.*\/.*)+',
-                stage= 'data', #'|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
+                stage= stage_id,
                 param = "default",
-                name= module_id # '|'.join([re.escape(x) for x in converter.get_initial_datasets()])
+                name= module_id 
             output:
-                "out/{stage}/{name}/{param}/{name}.dataext"
+                "out/{stage}/{name}/{param}/{name}.txt.gz",
+                "out/{stage}/{name}/{param}/{name}.meta.json",
+                "out/{stage}/{name}/{param}/{name}_params.txt"
             script:
                 op.join('src','do_something.py')
     elif converter.is_terminal(stage):
@@ -97,16 +98,16 @@ for node in G.nodes:
     else:
         rule:
             wildcard_constraints:
-                #pre = '(.*\/.*)+' <- we should fstring pre here using the parent's path
+                post = stage_id + '/' + module_id + '/' + param_id,
                 stage= stage_id, # '|'.join([re.escape(x) for x in converter.get_benchmark_stages()]),
                 module = module_id,
                 name='|'.join([re.escape(x) for x in converter.get_initial_datasets()]),
                 ext=".*$"
             name:  f"{{stage}}_{{module}}_{{param}}_run".format(stage=stage_id, module=module_id, param=param_id)
             input:
-                '{pre}/{name}.dataext'
+                '{pre}/{name}.txt.gz'                
             output:
-                "{pre}/{stage}/{module}/{params}/{name}.{ext}"
+                "{pre}/{post}/{name}.{ext}"
             script:
                 op.join("src", "do_something.py")