From a255f9152246549c0470772f7d0ce28618b3e368 Mon Sep 17 00:00:00 2001
From: jalil <jalil.nourisa@gmail.com>
Date: Wed, 4 Sep 2024 22:05:12 +0200
Subject: [PATCH] resources test are cleared. scenicplus and scglue fixed.
 sinlge omics workflow fixed

---
 .../multi_omics/scglue/config.vsh.yaml        |  2 +-
 src/methods/multi_omics/scglue/main.py        |  4 ++++
 .../single_omics/ennet/config.vsh.yaml        |  2 +-
 .../single_omics/genie3/config.vsh.yaml       |  2 +-
 .../single_omics/grnboost2/config.vsh.yaml    |  2 +-
 src/methods/single_omics/pidc/config.vsh.yaml |  2 +-
 .../single_omics/ppcor/config.vsh.yaml        |  2 +-
 .../single_omics/scsgl/config.vsh.yaml        |  2 +-
 .../single_omics/tigress/config.vsh.yaml      |  2 +-
 .../config.vsh.yaml                           |  2 +-
 .../run_benchmark_single_omics/main.nf        | 24 +++++++++----------
 11 files changed, 25 insertions(+), 21 deletions(-)

diff --git a/src/methods/multi_omics/scglue/config.vsh.yaml b/src/methods/multi_omics/scglue/config.vsh.yaml
index 71e4ac0bd..cfc0337a4 100644
--- 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
index fc6b450f3..b71a208e2 100644
--- 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
index b4f20a7a9..d775e3926 100644
--- 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
index 6aa4cdbb9..11c8077f2 100644
--- 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
index b9effc2dc..abed86fc4 100644
--- 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
index 00580a5b5..3da522615 100644
--- 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
index 4e6474973..de79446fe 100644
--- 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
index bff39ce3b..d781caff5 100644
--- 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
index 5ff3c6855..295bb3923 100644
--- 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
index b17a5ba8d..a69f4a320 100644
--- 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
index 2f5182517..d5ebaead0 100644
--- 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