diff --git a/picard.wdl b/picard.wdl index 5df7394b2ca252174f1d7429001ef347874998b2..6a52ee4c53a62a5b3b48a5cd1ed41838c2dd4e28 100644 --- a/picard.wdl +++ b/picard.wdl @@ -199,47 +199,6 @@ task CollectTargetedPcrMetrics { } } -task FixMateInformation { - input { - Array[File]+ inputBams - Array[File]+ inputBamsIndex - String outputBamPath - - String? preCommand - String? picardJar - - Int memory = 4 - Float memoryMultiplier = 3.0 - } - - String toolCommand = if defined(picardJar) - then "java -Xmx" + memory + "G -jar " + picardJar - else "picard -Xmx" + memory + "G" - - command { - set -e -o pipefail - ~{preCommand} - ~{toolCommand} \ - FixMateInformation \ - INPUT=~{sep=' INPUT=' inputBams} \ - OUTPUT=~{outputBamPath} \ - CREATE_INDEX=true \ - CREATE_MD5_FILE=true - } - - output { - IndexedBamFile outputBam = object { - file: outputBamPath, - index: sub(outputBamPath, ".bam$", ".bai"), - md5: outputBamPath + ".md5" - } - } - - runtime { - memory: ceil(memory * memoryMultiplier) - } -} - # Combine multiple recalibrated BAM files from scattered ApplyRecalibration runs task GatherBamFiles { input {