resources test are cleared. scenicplus and scglue fixed. sinlge omics…

… workflow fixed
openproblems-bio · Sep 4, 2024 · a255f91 · a255f91
1 parent 36b0fb4
commit a255f91
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Showing 11 changed files with 25 additions and 21 deletions.
diff --git a/src/methods/multi_omics/scglue/config.vsh.yaml b/src/methods/multi_omics/scglue/config.vsh.yaml
@@ -41,4 +41,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [oneweektime,midmem,highcpu]
+      label: [oneweektime, midmem, highcpu, gpu]
diff --git a/src/methods/multi_omics/scglue/main.py b/src/methods/multi_omics/scglue/main.py
@@ -257,6 +257,10 @@ def cis_inference(par):
 
 
 def main(par):
+    import torch
+    print("Is CUDA available:", torch.cuda.is_available())
+    print("Number of GPUs:", torch.cuda.device_count())
+
     os.makedirs(par['temp_dir'], exist_ok=True)
     print('Reading input files', flush=True)
     rna = ad.read_h5ad(par['multiomics_rna'])

diff --git a/src/methods/single_omics/ennet/config.vsh.yaml b/src/methods/single_omics/ennet/config.vsh.yaml
@@ -29,4 +29,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime,midmem,midcpu]
+      label: [threedaystime,midmem,midcpu]
diff --git a/src/methods/single_omics/genie3/config.vsh.yaml b/src/methods/single_omics/genie3/config.vsh.yaml
@@ -26,4 +26,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [midtime,midmem,midcpu]
+      label: [threedaystime, midmem,midcpu]
diff --git a/src/methods/single_omics/grnboost2/config.vsh.yaml b/src/methods/single_omics/grnboost2/config.vsh.yaml
@@ -26,4 +26,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime,midmem,midcpu]
+      label: [onedaytime, midmem, midcpu]
diff --git a/src/methods/single_omics/pidc/config.vsh.yaml b/src/methods/single_omics/pidc/config.vsh.yaml
@@ -22,4 +22,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [midtime,midmem,midcpu]
+      label: [threedaystime, midmem,midcpu]
diff --git a/src/methods/single_omics/ppcor/config.vsh.yaml b/src/methods/single_omics/ppcor/config.vsh.yaml
@@ -23,4 +23,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [midtime,midmem,midcpu]
+      label: [threedaystime, midmem,midcpu]
diff --git a/src/methods/single_omics/scsgl/config.vsh.yaml b/src/methods/single_omics/scsgl/config.vsh.yaml
@@ -28,4 +28,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime,midmem,midcpu]
+      label: [threedaystime, midmem,midcpu]
diff --git a/src/methods/single_omics/tigress/config.vsh.yaml b/src/methods/single_omics/tigress/config.vsh.yaml
@@ -26,4 +26,4 @@ platforms:
   - type: native
   - type: nextflow
     directives:
-      label: [onedaytime, midmem, highcpu]
+      label: [threedaystime, midmem, highcpu]
diff --git a/src/workflows/run_benchmark_single_omics/config.vsh.yaml b/src/workflows/run_benchmark_single_omics/config.vsh.yaml
@@ -87,4 +87,4 @@ functionality:
 platforms:
   - type: nextflow
     directives:
-      label: [ onedaytime, midmem, highcpu]
+      label: [ threedaystime, midmem, highcpu]
diff --git a/src/workflows/run_benchmark_single_omics/main.nf b/src/workflows/run_benchmark_single_omics/main.nf
@@ -12,25 +12,25 @@ workflow run_wf {
   main:
 
   // construct list of methods
+  methods = [
+    portia,
+    ennet,
+    genie3,
+    grnboost2,
+    pidc,
+    ppcor,
+    scsgl,
+    tigress
+  ]
+
   // methods = [
   //   portia,
   //   ennet,
-  //   genie3,
   //   grnboost2,
-  //   pidc,
-  //   ppcor,
-  //   scsgl,
+  //   scsgl,    
   //   tigress
   // ]
 
-  methods = [
-    portia,
-    // ennet
-    grnboost2
-    // scsgl,    
-    // tigress
-  ]
-
   // construct list of metrics
   metrics = [
     regression_1