fix: stub test

CCBR · Nov 29, 2023 · 971f08a · 971f08a
1 parent fc25c2d
commit 971f08a
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
@@ -20,12 +20,14 @@ jobs:
       run: |
         docker run -v $PWD:/opt2 nextflow/nextflow:22.10.8 \
         python /opt2/logan --fastq "/opt2/.tests/*R{1,2}.fastq.gz" \
+        --genome hg38 \
         --vc --sv --cnv \
         --output /opt2/output_tn_fqs \
         --sample_sheet "/opt2/.tests/pairs.tsv" --stub
     - name: Tumor-only FastQ Stub Run
       run: |
         docker run -v $PWD:/opt2 nextflow/nextflow:22.10.8 \
         python /opt2/logan --fastq "/opt2/.tests/*R{1,2}.fastq.gz" \
-        --vc \
+        --genome hg38 \
+        --vc --sv --cnv \
         --output /opt2/output_tonly_fqs --stub
diff --git a/logan b/logan
@@ -159,19 +159,18 @@ def main():
                 in1="--file_input "+args.file_input
     if (args.stub and args.profile is None): 
         profile="-profile localstub"
+        splitreg="4"
     elif args.profile=="local":
         profile="-profile local"
+        splitreg=str(args.splitregions)
     elif (args.profile=="biowulf" or args.profile is None):
         profile="-profile biowulf"
+        splitreg=str(args.splitregions)
     if args.resume:
         resume="-resume"
     else:
         resume=""
     ###COMBINE ALL COMMANDS (PIPE ALIGN)
-    if args.stub:
-        splitreg="4"
-    else:
-        splitreg=str(args.splitregions)
     commandbase=["nextflow run",dirname + '/main.nf',"-c "+ dirname +"/nextflow.config",
         in1,profile,resume,sample_path,"--genome",args.genome,
         "--output '" +args.output+"'"+" --split_regions " + splitreg]