From bfda9da2d9ef3ecd8be07c0e65730cd77de9a6a0 Mon Sep 17 00:00:00 2001
From: arontommi <arontommi@gmail.com>
Date: Sun, 29 Apr 2018 22:41:31 +0200
Subject: [PATCH] publishDir changed for process RunManta make sure bam files
 are not added to results file

---
 somaticVC.nf | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/somaticVC.nf b/somaticVC.nf
index 959519a6ab..e7fe0612cc 100644
--- 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([