pipelines_downsample_and_recall.cwl

Documentation for downsample_and_recall.cwl

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Overview

Downsample and HaplotypeCaller

Inputs

Name	Label	Description	Type	Secondary Files
reference		The reference that was used for the already-completed alignments	['string', 'File']
crams_to_downsample			{'type': 'array', 'items': {'type': 'record', 'name': 'crams', 'fields': {'cram': {'type': 'File'}, 'downsample_ratio': {'type': 'float', 'doc': 'the downsample ratio to use when reprocessing this CRAM'}, 'contamination': {'type': 'float', 'doc': 'contamination score to pass to HaplotypeCaller'}}}}
downsample_strategy			['null', {'type': 'enum', 'symbols': ['HighAccuracy', 'ConstantMemory', 'Chained']}]
downsample_seed			int?
emit_reference_confidence			{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']}
max_alternate_alleles			int?
ploidy			int?
read_filter			string?
intervals		arrays of intervals to use in each individual run of the haplotypecaller	{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
qc_minimum_mapping_quality			int
qc_minimum_base_quality			int

Outputs

Name	Label	Description	Type	Secondary Files
gvcfs			{'type': 'array', 'items': {'type': 'array', 'items': 'File'}}
wgs_metrics			File[]

Steps

Name	CWL Run
downsample	tools/downsample.cwl
haplotype_caller	subworkflows/gatk_haplotypecaller_iterator.cwl
collect_wgs_metrics	tools/collect_wgs_metrics.cwl