Fix FILTER_MAF process

Sage-Bionetworks-Workflows · Sep 19, 2022 · 2469a50 · 2469a50
1 parent f9fd807
commit 2469a50
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/bin/filter_maf.py b/bin/filter_maf.py
@@ -14,5 +14,5 @@
     writer = csv.DictWriter(outfile, reader.fieldnames, delimiter='\t')
     writer.writeheader()
     for row in reader:
-        if row['FILTER'] == 'PASS':
+        if row['FILTER'].lower().strip() in {'pass', '.', ''}:
             writer.writerow(row)
diff --git a/main.nf b/main.nf
@@ -102,7 +102,7 @@ process VCF2MAF {
 // Process for filtering MAF files for passed variants
 process FILTER_MAF {
 
-  tag "${input_maf.name}"
+  tag "${meta.synapse_id}"
 
   container "python:3.10.4"
 
@@ -203,12 +203,15 @@ workflow STUDY_MAFS {
     sample_mafs
 
   main:
+    // Only consider releasable MAF files
+    releasable_mafs = sample_mafs
+      .filter { meta, maf -> meta.is_releasable }
+
     // Filter MAF files for passed variants
-    FILTER_MAF(sample_mafs)
+    FILTER_MAF(releasable_mafs)
 
     // Group MAF files by study and merge
     mafs_by_study_ch = FILTER_MAF.out
-      .filter { meta, maf -> meta.is_releasable }
       .map { meta, maf -> subset_study_meta(meta, maf) }
       .groupTuple( by: 0 )
     MERGE_MAFS(mafs_by_study_ch)