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Commit eff1af58 authored by Ruben Vorderman's avatar Ruben Vorderman
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more sensible names

parent 43c38d8b
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1 merge request!21Added seqstat, set minlength for cutadapt to 1.
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biopet.wdl
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...@@ -280,7 +280,7 @@ task Seqstat { ...@@ -280,7 +280,7 @@ task Seqstat {
String? preCommand String? preCommand
File? toolJar File? toolJar
File fastq File fastq
String outputFile String outputFilePath
Float? memory Float? memory
Float? memoryMultiplier Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0])) Int mem = ceil(select_first([memory, 4.0]))
...@@ -292,13 +292,13 @@ task Seqstat { ...@@ -292,13 +292,13 @@ task Seqstat {
command { command {
set -e -o pipefail set -e -o pipefail
${preCommand} ${preCommand}
mkdir -p ${outputFile} mkdir -p ${outputFilePath}
${toolCommand} \ ${toolCommand} \
--fastq ${fastq} \ --fastq ${fastq} \
--output ${outputFile} --output ${outputFilePath}
} }
output { output {
File seqstatsJson = outputFile File json = outputFilePath
} }
runtime { runtime {
memory: ceil(mem * select_first([memoryMultiplier, 2.0])) memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
......
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