From 08aa335752d9206cffa735aaea91aeb8eac0e375 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 3 Sep 2018 16:09:03 +0200
Subject: [PATCH] fix/add somaticSeq output
---
somaticseq.wdl | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/somaticseq.wdl b/somaticseq.wdl
index dfd71e4..1b69518 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -60,8 +60,8 @@ task SomaticSeqWrapper {
output {
File consensusIndels = outputDir + "/Consensus.sINDEL.vcf"
File consensusSNV = outputDir + "/Consensus.sSNV.vcf"
- File ensembleIndels = outputDir + "/Ensemble.sINDEL.vcf"
- File ensembleSNV = outputDir + "/Ensemble.sSNV.vcf"
+ File ensembleIndels = outputDir + "/Ensemble.sINDEL.tsv"
+ File ensembleSNV = outputDir + "/Ensemble.sSNV.tsv"
}
}
@@ -104,4 +104,11 @@ task SsSomaticSeqWrapper {
~{"--scalpel " + scalpelVCF} \
~{"--strelka " + strelkaVCF}
}
+
+ output {
+ File consensusIndels = outputDir + "/Consensus.ssINDEL.vcf"
+ File consensusSNV = outputDir + "/Consensus.ssSNV.vcf"
+ File ensembleIndels = outputDir + "/Ensemble.ssINDEL.tsv"
+ File ensembleSNV = outputDir + "/Ensemble.ssSNV.tsv"
+ }
}
\ No newline at end of file
--
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