Merge pull request #579 from arontommi/master

Bam files for manta no longer saved (but still channeled to strelka)
SciLifeLab · Apr 30, 2018 · 36ddecf · 36ddecf
2 parents f4a2581 + bfda9da
commit 36ddecf
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/somaticVC.nf b/somaticVC.nf
@@ -532,8 +532,11 @@ if (params.verbose) strelkaOutput = strelkaOutput.view {
 process RunManta {
   tag {idSampleTumor + "_vs_" + idSampleNormal}
 
-  publishDir directoryMap.manta, mode: 'link'
-
+  publishDir directoryMap.manta, mode: 'link',
+      saveAs: {filename ->
+                  if (filename.endsWith(".bam") || filename.endsWith(".bai")) null
+                  else $filename
+                  }
   input:
     set idPatient, idSampleNormal, file(bamNormal), file(baiNormal), idSampleTumor, file(bamTumor), file(baiTumor) from bamsForManta
     set file(genomeFile), file(genomeIndex) from Channel.value([