From f368e6fa107bca8c25c8415828abc3144baf6469 Mon Sep 17 00:00:00 2001
From: jalil <jalil.nourisa@gmail.com>
Date: Sun, 1 Sep 2024 13:03:02 +0200
Subject: [PATCH] scenicplus integrated

---
 .../multi_omics/scenicplus/config.vsh.yaml    |  2 +-
 .../multi_omics/scenicplus_ns/config.vsh.yaml |  6 ++++++
 src/methods/multi_omics/scenicplus_ns/main.nf |  4 +---
 src/methods/multi_omics/scenicplus_ns/run.sh  | 20 +++++++++----------
 4 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/src/methods/multi_omics/scenicplus/config.vsh.yaml b/src/methods/multi_omics/scenicplus/config.vsh.yaml
index f4fbcdc36..77a37d0a0 100644
--- a/src/methods/multi_omics/scenicplus/config.vsh.yaml
+++ b/src/methods/multi_omics/scenicplus/config.vsh.yaml
@@ -24,7 +24,7 @@ functionality:
     - name: --cell_topic
       type: file 
       default: output/cell_topic.csv
-      required: true
+      required: false
       direction: output
       description: "Cell-topics prob scores"
   resources:
diff --git a/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml b/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml
index 9cf18f5e0..1fbcb40fe 100644
--- a/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml
+++ b/src/methods/multi_omics/scenicplus_ns/config.vsh.yaml
@@ -24,6 +24,12 @@ functionality:
       required: true
       direction: output
       description: "Cell-topics prob scores"
+    - name: --prediction
+      type: file 
+      default: output/prediction.csv
+      required: true
+      direction: output
+      description: "GRN"
 
   resources:
     - type: nextflow_script
diff --git a/src/methods/multi_omics/scenicplus_ns/main.nf b/src/methods/multi_omics/scenicplus_ns/main.nf
index 91fc79c75..4a27b82d0 100644
--- a/src/methods/multi_omics/scenicplus_ns/main.nf
+++ b/src/methods/multi_omics/scenicplus_ns/main.nf
@@ -10,9 +10,7 @@ workflow run_wf {
               multiomics_rna: "multiomics_rna",
               multiomics_atac: "multiomics_atac",
               temp_dir: "temp_dir",
-              num_workers: "num_workers",
-              scplus_mdata: "scplus_mdata", 
-              cell_topic: "cell_topic"
+              num_workers: "num_workers"
               
               ],
       toState: [prediction:"prediction", cell_topic:"cell_topic", scplus_mdata:"scplus_mdata"]
diff --git a/src/methods/multi_omics/scenicplus_ns/run.sh b/src/methods/multi_omics/scenicplus_ns/run.sh
index 05afe98dd..9c65bbb86 100644
--- a/src/methods/multi_omics/scenicplus_ns/run.sh
+++ b/src/methods/multi_omics/scenicplus_ns/run.sh
@@ -1,11 +1,11 @@
 #!/bin/bash
 
 RUN_ID="scenicplus"
-resources_dir="s3://openproblems-data/resources_test/grn"
-publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
+# resources_dir="s3://openproblems-data/resources_test/grn"
+# publish_dir="s3://openproblems-data/resources_test/grn/results/${RUN_ID}"
 
-# resources_dir="./resources_test"
-# publish_dir="./output/${RUN_ID}"
+resources_dir="./resources_test"
+publish_dir="./output/${RUN_ID}"
 
 num_workers=10
 
@@ -23,12 +23,12 @@ publish_dir: "$publish_dir"
 HERE
 
 
-# nextflow run . \
-#   -main-script  target/nextflow/workflows/grn_inference_scenicplus/main.nf \
-#   -profile docker \
-#   -with-trace \
-#   -c src/common/nextflow_helpers/labels_ci.config \
-#   -params-file params/${RUN_ID}.yaml
+nextflow run . \
+  -main-script  target/nextflow/workflows/grn_inference_scenicplus/main.nf \
+  -profile docker \
+  -with-trace \
+  -c src/common/nextflow_helpers/labels_ci.config \
+  -params-file params/${RUN_ID}.yaml
 
 
 # ./tw-windows-x86_64.exe launch `