diff --git a/picard.wdl b/picard.wdl index d5daa2487bc9e3ef403f1f9b22ff4801f1c4757b..04a750133e4b8524900ee3876d23ae0a9967839b 100644 --- a/picard.wdl +++ b/picard.wdl @@ -31,7 +31,7 @@ task BedToIntervalList { } parameter_meta { - bedfile: {description: "A bed file", category: "required"} + bedfile: {description: "A bed file.", category: "required"} dict: {description: "A sequence dict file.", category: "required"} outputPath: {description: "The location the output interval list should be written to.", category: "advanced"} @@ -147,21 +147,21 @@ task CollectMultipleMetrics { basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"} collectAlignmentSummaryMetrics: {description: "Equivalent to the `PROGRAM=CollectAlignmentSummaryMetrics` argument.", - category: "common"} + category: "advanced"} collectInsertSizeMetrics: {description: "Equivalent to the `PROGRAM=CollectInsertSizeMetrics` argument.", - category: "common"} + category: "advanced"} qualityScoreDistribution: {description: "Equivalent to the `PROGRAM=QualityScoreDistribution` argument.", - category: "common"} + category: "advanced"} meanQualityByCycle: {description: "Equivalent to the `PROGRAM=MeanQualityByCycle` argument.", - category: "common"} + category: "advanced"} collectBaseDistributionByCycle: {description: "Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.", - category: "common"} + category: "advanced"} collectGcBiasMetrics: {description: "Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.", - category: "common"} + category: "advanced"} collectSequencingArtifactMetrics: {description: "Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.", - category: "common"} + category: "advanced"} collectQualityYieldMetrics: {description: "Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.", - category: "common"} + category: "advanced"} memory: {description: "The amount of memory this job will use.", category: "advanced"} javaXmx: {description: "The maximum memory available to the program. (Should be lower than `memory` to accommodate JVM overhead.", @@ -210,10 +210,10 @@ task CollectRnaSeqMetrics { inputBam: {description: "The input BAM file for which metrics will be collected.", category: "required"} inputBamIndex: {description: "The index of the input BAM file.", category: "required"} - refRefflat: {description: "A refflat file containing gene annotations", catehory: "required"} + refRefflat: {description: "A refflat file containing gene annotations.", catehory: "required"} basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"} - strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics", + strandSpecificity: {description: "Equivalent to the `STRAND_SPECIFICITY` option of picard's CollectRnaSeqMetrics.", category: "common"} memory: {description: "The amount of memory this job will use.", category: "advanced"}