Merge pull request #579 from arontommi/master

Bam files for manta no longer saved (but still channeled to strelka)

Author: maxulysse

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([