diff --git a/picard.wdl b/picard.wdl index 104261816f42dea6126dc5c645ab7871e618fe1e..8177b2636a1546e0491af7449751c3ac441454c9 100644 --- a/picard.wdl +++ b/picard.wdl @@ -147,6 +147,40 @@ task MergeVCFs { File output_vcf_index = output_vcf_path + ".tbi" } + runtime { + memory: ceil(mem * select_first([memoryMultiplier, 1.5])) + } +} + +task SamToFastq { + String? preCommand + File inputBam + String outputRead1 + String? outputRead2 + String? outputUnpaired + String picard_jar + Float? memory + Float? memoryMultiplier + Int mem = ceil(select_first([memory, 4.0])) + + command { + set -e -o pipefail + ${preCommand} + java \ + -Xmx${mem}G \ + -jar ${picard_jar} \ + I=${inputBam} \ + ${"FASTQ=" + outputRead1} \ + ${"SECOND_END_FASTQ=" + outputRead2} \ + ${"UNPAIRED_FASTQ=" + outputUnpaired} + } + + output { + File read1 = outputRead1 + File? read2 = outputRead2 + File? unpairedRead = outputUnpaired + } + runtime { memory: ceil(mem * select_first([memoryMultiplier, 1.5])) }