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task SampleConfig {
input {
File? toolJar
String? preCommand
Array[File]+ inputFiles
String keyFilePath
String? sample
String? library
String? readgroup
String? jsonOutputPath
String? tsvOutputPath
Int memory = 4
Float memoryMultiplier = 2.0
}
String toolCommand = if defined(toolJar)
then "java -Xmx" + memory + "G -jar " +toolJar
else "biopet-sampleconfig -Xmx" + memory + "G"
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}
}
output {
File keysFile = keyFilePath
File? jsonOutput = jsonOutputPath
File? tsvOutput = tsvOutputPath
}
runtime {
memory: ceil(memory * memoryMultiplier)
}
}
task SampleConfigCromwellArrays {
input {
File? toolJar
String? preCommand
Array[File]+ inputFiles
String outputPath
Int memory = 4
Float memoryMultiplier = 2.0
}
String toolCommand = if defined(toolJar)
then "java -Xmx" + memory + "G -jar " + toolJar
else "biopet-sampleconfig -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputPath})
~{toolCommand} CromwellArrays \
-i ~{sep="-i " inputFiles} \
~{"-o " + outputPath}
}
output {
File outputFile = outputPath
}
runtime {
memory: ceil(memory * memoryMultiplier)
}
}
task CaseControl {
input {
File? toolJar
String? preCommand
Array[File]+ inputFiles
Array[File]+ sampleConfigs
String outputPath
String controlTag = "control"
Int memory = 4
Float memoryMultiplier = 1.5
}
String toolCommand = if defined(toolJar)
then "java -Xmx" + memory + "G -jar " + toolJar
else "biopet-sampleconfig -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{outputPath})
~{toolCommand} CromwellArrays \
-i ~{sep="-i " inputFiles} \
~{"-o " + outputPath} \
~{"--controlTag " + controlTag}
}
output {
File outputFile = outputPath
Array[CaseControl] caseControls = read_json(outputFile)
}
runtime {
memory: ceil(memory * memoryMultiplier)
}
}