pipelines_germline_exome_hla_typing.cwl

Documentation for germline_exome_hla_typing.cwl

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Overview

exome alignment and germline variant detection, with optitype for HLA typing

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[]
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[]?
bait_intervals			File
target_intervals			File
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[]
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?
vep_cache_dir			['string', 'Directory']
vep_ensembl_assembly		genome assembly to use in vep. Examples: GRCh38 or GRCm38	string
vep_ensembl_version		ensembl version - Must be present in the cache directory. Example: 95	string
vep_ensembl_species		ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus	string
synonyms_file			File?
annotate_coding_only			boolean?
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
qc_minimum_mapping_quality			int?
qc_minimum_base_quality			int?
optitype_name			string?

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
hs_metrics			File
per_target_coverage_metrics			File[]
per_target_hs_metrics			File[]
per_base_coverage_metrics			File[]
per_base_hs_metrics			File[]
summary_hs_metrics			File[]
flagstats			File
verify_bam_id_metrics			File
verify_bam_id_depth			File
raw_vcf			File	['.tbi']
final_vcf			File	['.tbi']
filtered_vcf			File	['.tbi']
vep_summary			File
optitype_tsv			File
optitype_plot			File

Steps

Name	CWL Run
germline_exome	pipelines/germline_exome.cwl
optitype	tools/optitype_dna.cwl