Inputs for GatkPreprocess
The following is an overview of all available inputs in GatkPreprocess.
Required inputs
- GatkPreprocess.bam
-
File
The BAM file which should be processed - GatkPreprocess.bamIndex
-
File
The index for the BAM file - GatkPreprocess.dbsnpVCF
-
File
A dbSNP vcf. - GatkPreprocess.dbsnpVCFIndex
-
File
Index for dbSNP vcf. - GatkPreprocess.referenceFasta
-
File
The reference fasta file - GatkPreprocess.referenceFastaDict
-
File
Sequence dictionary (.dict) for the reference fasta file - GatkPreprocess.referenceFastaFai
-
File
Fasta index (.fai) for the reference fasta file - GatkPreprocess.scatters
-
Array[File]
The bed files to be used
Other common inputs
- GatkPreprocess.bamName
-
String — Default:
"recalibrated"
The basename for the produced BAM files. This should not include any parent direcoties, use `outputDir` if the output directory should be changed. - GatkPreprocess.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - GatkPreprocess.splitSplicedReads
-
Boolean — Default:
false
Whether or not gatk's SplitNCgarReads should be run to split spliced reads. This should be enabled for RNAseq samples.
Advanced inputs
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- GatkPreprocess.applyBqsr.javaXmxMb
-
Int — Default:
2048
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.applyBqsr.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.baseRecalibrator.javaXmxMb
-
Int — Default:
1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.baseRecalibrator.knownIndelsSitesVCFIndexes
-
Array[File] — Default:
[]
The indexed for the known variant VCFs. - GatkPreprocess.baseRecalibrator.knownIndelsSitesVCFs
-
Array[File] — Default:
[]
VCF files with known indels. - GatkPreprocess.baseRecalibrator.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.23.2--0", "gatk4": "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - GatkPreprocess.gatherBamFiles.compressionLevel
-
Int?
The compression level of the output BAM. - GatkPreprocess.gatherBamFiles.createMd5File
-
Boolean — Default:
false
??? - GatkPreprocess.gatherBamFiles.javaXmxMb
-
Int — Default:
1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.gatherBamFiles.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.gatherBamFiles.timeMinutes
-
Int — Default:
1 + ceil((size(inputBams,"G") * 1))
The maximum amount of time the job will run in minutes. - GatkPreprocess.gatherBqsr.javaXmxMb
-
Int — Default:
256
The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead. - GatkPreprocess.gatherBqsr.memoryMb
-
Int — Default:
256 + javaXmxMb
The amount of memory this job will use in megabytes. - GatkPreprocess.gatherBqsr.timeMinutes
-
Int — Default:
1
The maximum amount of time the job will run in minutes. - GatkPreprocess.splitNCigarReads.javaXmx
-
String — Default:
"4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - GatkPreprocess.splitNCigarReads.memory
-
String — Default:
"5G"
The amount of memory this job will use.