diff --git a/picard.wdl b/picard.wdl index 6de0a614570b25b02cb2b9244a297644c40f88c6..6fcf6b6cfbf4e0e60df576e43f912caa2988f746 100644 --- a/picard.wdl +++ b/picard.wdl @@ -42,7 +42,7 @@ task BedToIntervalList { task CollectMultipleMetrics { input { String? preCommand - IndexedBamFile bam + IndexedBamFile bamFile Reference reference String basename @@ -72,7 +72,7 @@ task CollectMultipleMetrics { ~{preCommand} ~{toolCommand} \ CollectMultipleMetrics \ - I=~{bam.file} \ + I=~{bamFile.file} \ R=~{reference.fasta} \ O=~{basename} \ PROGRAM=null \ @@ -116,7 +116,7 @@ task CollectMultipleMetrics { task CollectRnaSeqMetrics { input { String? preCommand - IndexedBamFile bam + IndexedBamFile bamFile File refRefflat String basename String strandSpecificity = "NONE" @@ -137,7 +137,7 @@ task CollectRnaSeqMetrics { ~{preCommand} ~{toolCommand} \ CollectRnaSeqMetrics \ - I=~{bam.file} \ + I=~{bamFile.file} \ O=~{basename}.RNA_Metrics \ CHART_OUTPUT=~{basename}.RNA_Metrics.pdf \ STRAND_SPECIFICITY=~{strandSpecificity} \ @@ -157,7 +157,7 @@ task CollectRnaSeqMetrics { task CollectTargetedPcrMetrics { input { String? preCommand - IndexedBamFile bam + IndexedBamFile bamFile Reference reference File ampliconIntervals Array[File]+ targetIntervals @@ -179,7 +179,7 @@ task CollectTargetedPcrMetrics { ~{preCommand} ~{toolCommand} \ CollectTargetedPcrMetrics \ - I=~{bam.file} \ + I=~{bamFile.file} \ R=~{reference.fasta} \ AMPLICON_INTERVALS=~{ampliconIntervals} \ TARGET_INTERVALS=~{sep=" TARGET_INTERVALS=" targetIntervals} \