From 85cdcf20ec55379fe34ed74cf8d2925701ea7f7b Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 31 Jan 2018 11:52:32 +0100
Subject: [PATCH] remove pipeline specific command from samtools.wdl
---
bwa.wdl | 2 +-
samtools.wdl | 28 ----------------------------
2 files changed, 1 insertion(+), 29 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 6cd0cda..6f71b2f 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -83,7 +83,7 @@ task mem {
INPUT=/dev/stdin OUTPUT=${outputFile}
}
output {
- File samFile = select_first([outputFile])
+ File alignedFile = select_first([outputFile])
}
runtime {
cpu: select_first([threads])
diff --git a/samtools.wdl b/samtools.wdl
index 91fc317..e69de29 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -1,28 +0,0 @@
-task getContigMostCoverage {
- String? preCommand
- File bamFile
- String? outputFilePath = "mostCoveredContig.bam"
- command <<<
- set -e -o pipefail
- ${preCommand}
- samtools view -hb wgs1.bam $( \
- samtools idxstats wgs1.bam \
- | grep -ve "^\*" \
- | awk '{ print $1"\t"($3/$2)}' \
- | sort -rnk2 \
- | head -n 1 \
- | cut -f1) \
- > ${outputFilePath}
- samtools index ${outputFilePath}
- >>>
-
- output {
- File contig = outputFilePath
- }
-
- parameter_meta {
- preCommand: "This command is run before running the samtools command. Can be used to set up environments such as conda."
- bamFile: "Must be a sorted BAM file with an index"
- outputFilePath: "where the output file is stored"
- }
-}
\ No newline at end of file
--
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