diff --git a/picard.wdl b/picard.wdl index 144c778260b39f1942942a8040a3200d1b7e876f..e81cd4e3b8eda17f3286e4979d7b5dc971e4f6a2 100644 --- a/picard.wdl +++ b/picard.wdl @@ -1038,6 +1038,7 @@ task UmiAwareMarkDuplicatesWithMateCigar { String outputPath String outputPathMetrics = outputPath + ".metrics" String outputPathUmiMetrics = outputPath + ".umi-metrics" + Int maxRecordsInRam = 3000000 # Default is 500_000 but that will lead to very small files on disk. String? assumeSortOrder String tempdir = "temp" Boolean removeDuplicates = true @@ -1063,6 +1064,7 @@ task UmiAwareMarkDuplicatesWithMateCigar { UMI_METRICS_FILE=~{outputPathUmiMetrics} \ TMP_DIR=~{tempdir} \ REMOVE_DUPLICATES=~{removeDuplicates} \ + MAX_RECORDS_IN_RAM=~{maxRecordsInRam} \ CREATE_INDEX=true \ COMPRESSION_LEVEL=~{compressionLevel} \ USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \