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Commit 8bb2dc43 authored by Ruben Vorderman's avatar Ruben Vorderman
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star to 1.0

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1 merge request!34Move all files to version 1.0
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version 1.0
task Star { task Star {
String? preCommand input {
String? preCommand
Array[File] inputR1 Array[File] inputR1
Array[File]? inputR2 Array[File]? inputR2
String genomeDir String genomeDir
String outFileNamePrefix String outFileNamePrefix
String? outSAMtype String? outSAMtype
String? readFilesCommand String? readFilesCommand
Int? runThreadN Int? runThreadN
String? outStd String? outStd
String? twopassMode String? twopassMode
Array[String]? outSAMattrRGline Array[String]? outSAMattrRGline
Int? limitBAMsortRAM Int? limitBAMsortRAM
Int? memory Int? memory
}
#TODO needs to be extended for all possible output extensions #TODO needs to be extended for all possible output extensions
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"} Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
...@@ -24,19 +28,19 @@ task Star { ...@@ -24,19 +28,19 @@ task Star {
command { command {
set -e -o pipefail set -e -o pipefail
mkdir -p ${sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")} mkdir -p ~{sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
${preCommand} ~{preCommand}
STAR \ STAR \
--readFilesIn ${sep=',' inputR1} ${sep="," inputR2} \ --readFilesIn ~{sep=',' inputR1} ~{sep="," inputR2} \
--outFileNamePrefix ${outFileNamePrefix} \ --outFileNamePrefix ~{outFileNamePrefix} \
--genomeDir ${genomeDir} \ --genomeDir ~{genomeDir} \
--outSAMtype ${default="BAM SortedByCoordinate" outSAMtype} \ --outSAMtype ~{default="BAM SortedByCoordinate" outSAMtype} \
--readFilesCommand ${default="zcat" readFilesCommand} \ --readFilesCommand ~{default="zcat" readFilesCommand} \
${"--runThreadN " + runThreadN} \ ~{"--runThreadN " + runThreadN} \
${"--outStd " + outStd} \ ~{"--outStd " + outStd} \
${"--twopassMode " + twopassMode} \ ~{"--twopassMode " + twopassMode} \
${"--limitBAMsortRAM " + limitBAMsortRAM} \ ~{"--limitBAMsortRAM " + limitBAMsortRAM} \
${true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ${sep=" , " outSAMattrRGline} ~{true="--outSAMattrRGline " false="" defined(outSAMattrRGline)} ~{sep=" , " outSAMattrRGline}
} }
output { output {
...@@ -50,13 +54,14 @@ task Star { ...@@ -50,13 +54,14 @@ task Star {
} }
task makeStarRGline { task makeStarRGline {
String sample input {
String library String sample
String? platform String library
String readgroup String? platform
String readgroup
}
command { command {
printf '"ID:${readgroup}" "LB:${library}" "PL:${default="ILLUMINA" platform}" "SM:${sample}"' printf '"ID:~{readgroup}" "LB:~{library}" "PL:~{default="ILLUMINA" platform}" "SM:~{sample}"'
} }
output { output {
......
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