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gatk-indelrealigner.cwl.yaml
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cwlVersion: v1.0
class: CommandLineTool
label: GATK IndelRealigner
hints:
- class: ResourceRequirement
coresMin: 8
ramMin: 32
requirements:
- class: DockerRequirement
dockerPull: "opengenomics/gatk-cocleaning:latest"
baseCommand:
- "java"
- "-jar"
- "/opt/GenomeAnalysisTK.jar"
- "-T"
- "IndelRealigner"
- "--disable_auto_index_creation_and_locking_when_reading_rods"
arguments:
- valueFrom: .realigned.bam
prefix: -nWayOut
inputs:
tumor_bam:
type: File
inputBinding:
prefix: -I
doc: bam file produced after markDups execution
secondaryFiles:
- .bai
normal_bam:
type: File?
inputBinding:
prefix: -I
doc: bam file produced after markDups execution
secondaryFiles:
- .bai
knownIndels:
type:
- "null"
- type: array
items: File
inputBinding:
prefix: --knownAlleles
inputBinding:
position: 1
secondaryFiles:
- .tbi
doc: Any number of VCF files representing known SNPs and/or indels. Could be e.g.
dbSNP and/or official 1000 Genomes indel calls. SNPs in these files will be
ignored unless the --mismatchFraction argument is used. optional parameter.
reference:
type: File
inputBinding:
prefix: -R
secondaryFiles:
- .fai
- ^.dict
intervals:
type: File
inputBinding:
prefix: --targetIntervals
doc: list of intervals created by realignerTargetCreataor
maxReadsForConsensuses:
type: int?
inputBinding:
prefix: --maxReadsForConsensuses
doc: Max reads used for finding the alternate consensuses (necessary to improve
performance in deep coverage)
LODThresholdForCleaning:
type: double?
inputBinding:
prefix: --LODThresholdForCleaning
doc: LOD threshold above which the cleaner will clean
maxConsensuses:
type: int?
inputBinding:
prefix: --maxConsensuses
doc: Max alternate consensuses to try (necessary to improve performance in deep
coverage)
maxReadsInMemory:
type: int?
inputBinding:
prefix: --maxReadsInMemory
doc: max reads allowed to be kept in memory at a time by the SAMFileWriter
maxIsizeForMovement:
type: int?
inputBinding:
prefix: --maxIsizeForMovement
doc: maximum insert size of read pairs that we attempt to realign. For expert
users only!
maxPositionalMoveAllowed:
type: int?
inputBinding:
prefix: --maxPositionalMoveAllowed
doc: Maximum positional move in basepairs that a read can be adjusted during realignment.
For expert users only!
entropyThreshold:
type: double?
inputBinding:
prefix: --entropyThreshold
doc: Percentage of mismatches at a locus to be considered having high entropy
(0.0 < entropy <= 1.0)
maxReadsForRealignment:
type: int?
inputBinding:
prefix: --maxReadsForRealignment
doc: Max reads allowed at an interval for realignment
consensusDeterminationModel:
type: string?
inputBinding:
prefix: --consensusDeterminationModel
doc: Percentage of mismatches at a locus to be considered having high entropy
(0.0 < entropy <= 1.0)
noOriginalAlignmentTags:
type: boolean?
inputBinding:
prefix: --noOriginalAlignmentTags
doc: Dont output the original cigar or alignment start tags for each realigned
read in the output bam
outputs:
tumor_realigned:
type: File
outputBinding:
glob: $(inputs.tumor_bam.nameroot).realigned.bam
secondaryFiles:
- ^.bai
normal_realigned:
type: File
outputBinding:
glob: $(inputs.normal_bam.nameroot).realigned.bam
secondaryFiles:
- ^.bai