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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 {
String? preCommand
File? toolJar
File fastq
String outputFilePath
String outputFile
Float? memory
Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
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"
command {
set -e -o pipefail
${preCommand}
mkdir -p $(dirname ${outputFilePath})
mkdir -p $(dirname ${outputFile})
${toolCommand} \
--fastq ${fastq} \
--output ${outputFilePath}
--output ${outputFile}
}
output {
File json = outputFilePath
File json = outputFile
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
......
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