diff --git a/picard.wdl b/picard.wdl index d8ce5ebe14afbb47df8af20c8f39fda6f500bc93..d2a6ca35d9561cfda9713ad14be474fa5acbc635 100644 --- a/picard.wdl +++ b/picard.wdl @@ -1007,7 +1007,7 @@ task RenameSample { task UmiAwareMarkDuplicatesWithMateCigar { input { - File inputBam + Array[File] inputBams String outputPath String outputPathMetrics = outputPath + ".metrics" String outputPathUmiMetrics = outputPath + ".umi-metrics" @@ -1023,7 +1023,7 @@ task UmiAwareMarkDuplicatesWithMateCigar { set -e mkdir -p "$(dirname ~{outputPath})" ~{tempdir} picard UmiAwareMarkDuplicatesWithMateCigar \ - I=~{inputBam} \ + INPUT=~{sep=' INPUT=' inputBams} \ O=~{outputPath} \ M=~{outputPathMetrics} \ UMI_METRICS_FILE=~{outputPathUmiMetrics} \ @@ -1047,7 +1047,7 @@ task UmiAwareMarkDuplicatesWithMateCigar { parameter_meta { # inputs - inputBam: {description: "The unsorted input BAM file.", category: "required"} + inputBams: {description: "The BAM files for which the duplicate reads should be marked.", category: "required"} outputPath: {description: "The location the output BAM file should be written to.", category: "required"} outputPathMetrics: {description: "The location the output metrics file should be written to.", category: "required"} outputPathUmiMetrics: {description: "The location the output UMI metrics file should be written to.", category: "required"}