From 2de46d0afaf2d3d7704b9dc33825f4dc3be06aef Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 23 Jul 2018 13:08:25 +0200
Subject: [PATCH] new style variable things
---
bioconda.wdl | 8 +--
biopet.wdl | 138 +++++++++++++++++++++++++--------------------------
2 files changed, 73 insertions(+), 73 deletions(-)
diff --git a/bioconda.wdl b/bioconda.wdl
index 13cab3a..6dc62b3 100644
--- a/bioconda.wdl
+++ b/bioconda.wdl
@@ -9,8 +9,8 @@ task installPrefix {
String prefix
String? condaPath
}
- command {
- ${default="conda" condaPath} create \
+ command <<<
+ ~{default="conda" condaPath} create \
--json -q \
--yes \
--override-channels \
@@ -19,8 +19,8 @@ task installPrefix {
--channel defaults \
--channel r \
--prefix ${prefix} \
- ${sep=' ' requirements}
- }
+ ~{sep=' ' requirements}
+ >>>
output {
File condaEnvPath=prefix
File condaJson=stdout()
diff --git a/biopet.wdl b/biopet.wdl
index bde7390..8b1d865 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -21,13 +21,13 @@ task BaseCounter {
command {
set -e -o pipefail
- mkdir -p ${outputDir}
- ${preCommand}
- ${toolCommand} \
- -b ${bam} \
- -r ${refFlat} \
- -o ${outputDir} \
- -p ${prefix}
+ mkdir -p ~{outputDir}
+ ~{preCommand}
+ ~{toolCommand} \
+ -b ~{bam} \
+ -r ~{refFlat} \
+ -o ~{outputDir} \
+ -p ~{prefix}
}
output {
@@ -97,17 +97,17 @@ task ExtractAdaptersFastqc {
command {
set -e
- ${preCommand}
- mkdir -p ${outputDir}
- ${toolCommand} \
- --inputFile ${inputFile} \
- ${"--adapterOutputFile " + adapterOutputFilePath } \
- ${"--contamsOutputFile " + contamsOutputFilePath } \
- ${"--knownContamFile " + knownContamFile} \
- ${"--knownAdapterFile " + knownAdapterFile} \
- ${"--adapterCutoff " + adapterCutoff} \
- ${true="--skipContams" false="" skipContams} \
- ${true="--outputAsFasta" false="" outputAsFasta}
+ ~{preCommand}
+ mkdir -p ~{outputDir}
+ ~{toolCommand} \
+ --inputFile ~{inputFile} \
+ ~{"--adapterOutputFile " + adapterOutputFilePath } \
+ ~{"--contamsOutputFile " + contamsOutputFilePath } \
+ ~{"--knownContamFile " + knownContamFile} \
+ ~{"--knownAdapterFile " + knownAdapterFile} \
+ ~{"--adapterCutoff " + adapterCutoff} \
+ ~{true="--skipContams" false="" skipContams} \
+ ~{true="--outputAsFasta" false="" outputAsFasta}
}
output {
@@ -140,14 +140,14 @@ task FastqSplitter {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p $(dirname ${sep=') $(dirname ' outputPaths})
- if [ ${length(outputPaths)} -gt 1 ]; then
- ${toolCommand} \
- -I ${inputFastq} \
- -o ${sep=' -o ' outputPaths}
+ ~{preCommand}
+ mkdir -p $(dirname ~{sep=') $(dirname ' outputPaths})
+ if [ ~{length(outputPaths)} -gt 1 ]; then
+ ~{toolCommand} \
+ -I ~{inputFastq} \
+ -o ~{sep=' -o ' outputPaths}
else
- ln -sf ${inputFastq} ${outputPaths[0]}
+ ln -sf ~{inputFastq} ~{outputPaths[0]}
fi
}
@@ -182,15 +182,15 @@ task FastqSync {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p $(dirname ${out1path}) $(dirname ${out2path})
- ${toolCommand} \
- --in1 ${in1} \
- --in2 ${in2} \
- --ref1 ${ref1} \
- --ref2 ${ref2} \
- --out1 ${out1path} \
- --out2 ${out2path}
+ ~{preCommand}
+ mkdir -p $(dirname ~{out1path}) $(dirname ~{out2path})
+ ~{toolCommand} \
+ --in1 ~{in1} \
+ --in2 ~{in2} \
+ --ref1 ~{ref1} \
+ --ref2 ~{ref2} \
+ --out1 ~{out1path} \
+ --out2 ~{out2path}
}
output {
@@ -226,16 +226,16 @@ task SampleConfig {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
- ${toolCommand} \
- -i ${sep="-i " inputFiles} \
- ${"--sample " + sample} \
- ${"--library " + library} \
- ${"--readgroup " + readgroup} \
- ${"--jsonOutput " + jsonOutputPath} \
- ${"--tsvOutput " + tsvOutputPath} \
- > ${keyFilePath}
+ ~{preCommand}
+ mkdir -p . ~{"$(dirname " + jsonOutputPath + ")"} ~{"$(dirname " + tsvOutputPath + ")"}
+ ~{toolCommand} \
+ -i ~{sep="-i " inputFiles} \
+ ~{"--sample " + sample} \
+ ~{"--library " + library} \
+ ~{"--readgroup " + readgroup} \
+ ~{"--jsonOutput " + jsonOutputPath} \
+ ~{"--tsvOutput " + tsvOutputPath} \
+ > ~{keyFilePath}
}
output {
@@ -270,13 +270,13 @@ task ScatterRegions {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p ${outputDirPath}
- ${toolCommand} \
- -R ${refFasta} \
- -o ${outputDirPath} \
- ${"-s " + scatterSize} \
- ${"-L " + regions}
+ ~{preCommand}
+ mkdir -p ~{outputDirPath}
+ ~{toolCommand} \
+ -R ~{refFasta} \
+ -o ~{outputDirPath} \
+ ~{"-s " + scatterSize} \
+ ~{"-L " + regions}
}
output {
@@ -305,11 +305,11 @@ task Seqstat {
command {
set -e -o pipefail
- ${preCommand}
- mkdir -p $(dirname ${outputFile})
- ${toolCommand} \
- --fastq ${fastq} \
- --output ${outputFile}
+ ~{preCommand}
+ mkdir -p $(dirname ~{outputFile})
+ ~{toolCommand} \
+ --fastq ~{fastq} \
+ --output ~{outputFile}
}
output {
@@ -339,11 +339,11 @@ task ValidateAnnotation {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand} \
- ${"-r" + refRefflat} \
- ${"-g" + gtfFile} \
- -R ${refFasta}
+ ~{preCommand}
+ ~{toolCommand} \
+ ~{"-r" + refRefflat} \
+ ~{"-g" + gtfFile} \
+ -R ~{refFasta}
}
output {
@@ -373,10 +373,10 @@ task ValidateFastq {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand}\
- --fastq1 ${fastq1} \
- ${"--fastq2 " + fastq2}
+ ~{preCommand}
+ ~{toolCommand}\
+ --fastq1 ~{fastq1} \
+ ~{"--fastq2 " + fastq2}
}
output {
@@ -406,10 +406,10 @@ task ValidateVcf {
command {
set -e -o pipefail
- ${preCommand}
- ${toolCommand}\
- -i ${vcfFile} \
- -R ${refFasta}
+ ~{preCommand}
+ ~{toolCommand}\
+ -i ~{vcfFile} \
+ -R ~{refFasta}
}
output {
--
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