From 6c2f89bb6d4a7a7c8fb4f2235d5c783a5b819ecc Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 31 Jan 2018 11:25:59 +0100
Subject: [PATCH] add task to get contig with most coverage
---
samtools.wdl | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 samtools.wdl
diff --git a/samtools.wdl b/samtools.wdl
new file mode 100644
index 0000000..d3cd5f1
--- /dev/null
+++ b/samtools.wdl
@@ -0,0 +1,24 @@
+task getContigMostCoverage {
+ String? preCommand
+ File bamFile
+ String? outputFilePath = "output.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}
+ >>>
+
+ 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
--
GitLab