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Inputs for BamMetrics

The following is an overview of all available inputs in BamMetrics.

Required inputs

BamMetrics.bam: File
The BAM file for which metrics will be collected.
BamMetrics.bamIndex: File
The index for the bam file.
BamMetrics.referenceFasta: File
The reference fasta file.
BamMetrics.referenceFastaDict: File
The sequence dictionary associated with the reference fasta file.
BamMetrics.referenceFastaFai: File
The index for the reference fasta file.

Other common inputs

BamMetrics.ampliconIntervals: File?
An interval list describinig the coordinates of the amplicons sequenced. This should only be used for targeted sequencing or WES. Required if `ampliconIntervals` is defined.
BamMetrics.outputDir: String — Default: "."
The directory to which the outputs will be written.
BamMetrics.refRefflat: File?
A refflat file containing gene annotations. If defined RNA sequencing metrics will be collected.
BamMetrics.strandedness: String — Default: "None"
The strandedness of the RNA sequencing library preparation. One of "None" (unstranded), "FR" (forward-reverse: first read equal transcript) or "RF" (reverse-forward: second read equals transcript).
BamMetrics.targetIntervals: Array[File]+?
An interval list describing the coordinates of the targets sequenced. This should only be used for targeted sequencing or WES. If defined targeted PCR metrics will be collected. Requires `ampliconIntervals` to also be defined.

Advanced inputs

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BamMetrics.ampliconIntervalsLists.javaXmx: String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
BamMetrics.ampliconIntervalsLists.memory: String — Default: "4GiB"
The amount of memory this job will use.
BamMetrics.ampliconIntervalsLists.timeMinutes: Int — Default: 5
The maximum amount of time the job will run in minutes.
BamMetrics.collectAlignmentSummaryMetrics: Boolean — Default: true
Equivalent to the `PROGRAM=CollectAlignmentSummaryMetrics` argument in Picard.
BamMetrics.dockerImages: Map[String,String] — Default: {"samtools": "quay.io/biocontainers/samtools:1.11--h6270b1f_0", "picard": "quay.io/biocontainers/picard:2.23.8--0"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
BamMetrics.Flagstat.memory: String — Default: "256MiB"
The amount of memory needed for the job.
BamMetrics.Flagstat.timeMinutes: Int — Default: 1 + ceil(size(inputBam,"G"))
The maximum amount of time the job will run in minutes.
BamMetrics.meanQualityByCycle: Boolean — Default: true
Equivalent to the `PROGRAM=MeanQualityByCycle` argument in Picard.
BamMetrics.picardMetrics.collectBaseDistributionByCycle: Boolean — Default: true
Equivalent to the `PROGRAM=CollectBaseDistributionByCycle` argument.
BamMetrics.picardMetrics.collectGcBiasMetrics: Boolean — Default: true
Equivalent to the `PROGRAM=CollectGcBiasMetrics` argument.
BamMetrics.picardMetrics.collectInsertSizeMetrics: Boolean — Default: true
Equivalent to the `PROGRAM=CollectInsertSizeMetrics` argument.
BamMetrics.picardMetrics.collectQualityYieldMetrics: Boolean — Default: true
Equivalent to the `PROGRAM=CollectQualityYieldMetrics` argument.
BamMetrics.picardMetrics.collectSequencingArtifactMetrics: Boolean — Default: true
Equivalent to the `PROGRAM=CollectSequencingArtifactMetrics` argument.
BamMetrics.picardMetrics.javaXmxMb: Int — Default: 3072
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.
BamMetrics.picardMetrics.memoryMb: Int — Default: javaXmxMb + 512
The amount of memory this job will use in megabytes.
BamMetrics.picardMetrics.qualityScoreDistribution: Boolean — Default: true
Equivalent to the `PROGRAM=QualityScoreDistribution` argument.
BamMetrics.picardMetrics.timeMinutes: Int — Default: 1 + ceil((size(referenceFasta,"GiB") * 3 * 2)) + ceil((size(inputBam,"GiB") * 6))
The maximum amount of time the job will run in minutes.
BamMetrics.rnaSeqMetrics.javaXmx: String — Default: "8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
BamMetrics.rnaSeqMetrics.memory: String — Default: "9GiB"
The amount of memory this job will use.
BamMetrics.rnaSeqMetrics.timeMinutes: Int — Default: 1 + ceil((size(inputBam,"GiB") * 12))
The maximum amount of time the job will run in minutes.
BamMetrics.targetIntervalsLists.javaXmx: String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
BamMetrics.targetIntervalsLists.memory: String — Default: "4GiB"
The amount of memory this job will use.
BamMetrics.targetIntervalsLists.timeMinutes: Int — Default: 5
The maximum amount of time the job will run in minutes.
BamMetrics.targetMetrics.javaXmx: String — Default: "3G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
BamMetrics.targetMetrics.memory: String — Default: "4GiB"
The amount of memory this job will use.
BamMetrics.targetMetrics.timeMinutes: Int — Default: 1 + ceil((size(inputBam,"GiB") * 6))
The maximum amount of time the job will run in minutes.

BioWDL: BamMetrics

Inputs for BamMetrics

Required inputs

Other common inputs

Advanced inputs