scenicplus integrated

openproblems-bio · Sep 1, 2024 · f368e6f · f368e6f
1 parent 87cc0ed
commit f368e6f
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Showing 4 changed files with 18 additions and 14 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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 `