pipelines_germline_wgs_gvcf.cwl

Documentation for germline_wgs_gvcf.cwl

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Overview

wgs alignment and germline variant detection

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa']
sequence	sequence: sequencing data and readgroup information	sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.	../types/sequence_data.yml#sequence_data[]
trimming			['../types/trimming_options.yml#trimming_options', 'null']
omni_vcf			File	['.tbi']
picard_metric_accumulation_level			string
emit_reference_confidence			{'type': 'enum', 'symbols': ['NONE', 'BP_RESOLUTION', 'GVCF']}
gvcf_gq_bands			string[]
intervals			{'type': 'array', 'items': {'type': 'array', 'items': 'string'}}
ploidy			int?
qc_intervals			File
synonyms_file			File?
annotate_coding_only			boolean?
bqsr_known_sites		One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.	File[]	['.tbi']
bqsr_intervals			string[]?
minimum_mapping_quality			int?
minimum_base_quality			int?
per_base_intervals			../types/labelled_file.yml#labelled_file[]
per_target_intervals			../types/labelled_file.yml#labelled_file[]
summary_intervals			../types/labelled_file.yml#labelled_file[]

Outputs

Name	Label	Description	Type	Secondary Files
cram			File
mark_duplicates_metrics			File
insert_size_metrics			File
insert_size_histogram			File
alignment_summary_metrics			File
gc_bias_metrics			File
gc_bias_metrics_chart			File
gc_bias_metrics_summary			File
wgs_metrics			File
flagstats			File
verify_bam_id_metrics			File
verify_bam_id_depth			File
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
summary_hs_metrics			File[]
gvcf			File[]

Steps

Name	CWL Run
alignment_and_qc	pipelines/alignment_wgs.cwl
extract_freemix
generate_gvcfs	subworkflows/gatk_haplotypecaller_iterator.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl