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.