Please be aware that the page you are currently viewing is not for the latest available version!
Inputs for BamMetrics
The following is an overview of all available inputs in BamMetrics.
Required inputs
- BamMetrics.bam
-
struct(file : File, index : File, md5sum : String?) — Default:
None
??? - BamMetrics.reference
-
struct(dict : File, fai : File, fasta : File) — Default:
None
???
Other inputs
Show/Hide
- BamMetrics.ampliconIntervals
-
File? — Default:
None
??? - BamMetrics.ampliconIntervalsLists.javaXmx
-
String — Default:
"4G"
??? - BamMetrics.ampliconIntervalsLists.memory
-
String — Default:
"12G"
??? - BamMetrics.dockerImages
-
Map[String,String] — Default:
{"samtools": "quay.io/biocontainers/samtools:1.8--h46bd0b3_5", "picard": "quay.io/biocontainers/picard:2.20.5--0"}
??? - BamMetrics.outputDir
-
String — Default:
"."
??? - BamMetrics.picardMetrics.collectAlignmentSummaryMetrics
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.collectBaseDistributionByCycle
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.collectGcBiasMetrics
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.collectInsertSizeMetrics
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.collectQualityYieldMetrics
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.collectSequencingArtifactMetrics
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.javaXmx
-
String — Default:
"8G"
??? - BamMetrics.picardMetrics.meanQualityByCycle
-
Boolean — Default:
true
??? - BamMetrics.picardMetrics.memory
-
String — Default:
"32G"
??? - BamMetrics.picardMetrics.qualityScoreDistribution
-
Boolean — Default:
true
??? - BamMetrics.refRefflat
-
File? — Default:
None
??? - BamMetrics.rnaSeqMetrics.javaXmx
-
String — Default:
"8G"
??? - BamMetrics.rnaSeqMetrics.memory
-
String — Default:
"32G"
??? - BamMetrics.strandedness
-
String — Default:
"None"
??? - BamMetrics.targetIntervals
-
Array[File]+? — Default:
None
??? - BamMetrics.targetIntervalsLists.javaXmx
-
String — Default:
"4G"
??? - BamMetrics.targetIntervalsLists.memory
-
String — Default:
"12G"
??? - BamMetrics.targetMetrics.javaXmx
-
String — Default:
"4G"
??? - BamMetrics.targetMetrics.memory
-
String — Default:
"12G"
???