tools_vep.cwl

Documentation for vep.cwl

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Overview

Ensembl Variant Effect Predictor

Docker Requirement

mgibio/vep_helper-cwl:1.1.0

Inputs

Name	Label	Description	Type	Secondary Files
vcf			File
cache_dir			string
synonyms_file			File?
coding_only			boolean
pick			['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}]
custom_annotations			['null', {'type': 'array', 'items': '../types/vep_custom_annotation.yml#vep_custom_annotation', 'label': 'custom type, check types directory for input format', 'inputBinding': {'valueFrom': "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n", 'position': 6}}]
reference			['null', 'string', 'File']	['.fai', '^.dict']
plugins			{'type': 'array', 'items': 'string', 'inputBinding': {'prefix': '--plugin'}}
everything			boolean?
ensembl_assembly		genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'	string
ensembl_version		ensembl version - Must be present in the cache directory. Example: '95'	string
ensembl_species		ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'	string

Outputs

Name	Label	Description	Type	Secondary Files
annotated_vcf			File
vep_summary			File