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Commit 9253f307 authored by Ruben Vorderman's avatar Ruben Vorderman
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fix review points

parent 5ddecde6
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1 merge request!21Added seqstat, set minlength for cutadapt to 1.
...@@ -280,25 +280,25 @@ task Seqstat { ...@@ -280,25 +280,25 @@ task Seqstat {
String? preCommand String? preCommand
File? toolJar File? toolJar
File fastq File fastq
String outputFilePath String outputFile
Float? memory Float? memory
Float? memoryMultiplier Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0])) Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar) String toolCommand = if defined(toolJar)
then "java -Xmx" + mem + "G -jar " +toolJar then "java -Xmx" + mem + "G -jar " + toolJar
else "biopet-seqstat -Xmx" + mem + "G" else "biopet-seqstat -Xmx" + mem + "G"
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
mkdir -p $(dirname ${outputFilePath}) mkdir -p $(dirname ${outputFile})
${toolCommand} \ ${toolCommand} \
--fastq ${fastq} \ --fastq ${fastq} \
--output ${outputFilePath} --output ${outputFile}
} }
output { output {
File json = outputFilePath File json = outputFile
} }
runtime { runtime {
memory: ceil(mem * select_first([memoryMultiplier, 2.0])) memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
......
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