diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl new file mode 100644 index 0000000000000000000000000000000000000000..20099757e44bd09acd100e7ba79a98412d83d869 --- /dev/null +++ b/biopet/seqstat.wdl @@ -0,0 +1,40 @@ +task Generate { + input { + String? preCommand + File? toolJar + File fastqR1 + File fastqR2 + String outputFile + String? sample + String? library + String? readgroup + + Int memory = 4 + Float memoryMultiplier = 2.0 + } + + String toolCommand = if defined(toolJar) + then "java -Xmx" + memory + "G -jar " + toolJar + else "biopet-seqstat -Xmx" + memory + "G" + + command { + set -e -o pipefail + ~{preCommand} + mkdir -p $(dirname ~{outputFile}) + ~{toolCommand} \ + --fastqR1 ~{fastqR1} \ + --fastqR2 ~{fastqR2} \ + --output ~{outputFile} \ + ~{"--sample " + sample} \ + ~{"--library " + library } \ + ~{"--readgroup " + readgroup } + } + + output { + File json = outputFile + } + + runtime { + memory: ceil(memory * memoryMultiplier) + } +} \ No newline at end of file