pipelines_tumor_only_detect_variants.cwl

Documentation for tumor_only_detect_variants.cwl

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Overview

Tumor-Only Detect Variants workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
bam			File	['^.bai', '.bai']
roi_intervals	roi_intervals: regions of interest in which variants will be called	roi_intervals is a list of regions (in interval_list format) within which to call somatic variants	File
varscan_strand_filter			int?
varscan_min_coverage			int?
varscan_min_var_freq			float?
varscan_p_value			float?
varscan_min_reads			int?
maximum_population_allele_frequency			float?
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_pick			['null', {'type': 'enum', 'symbols': ['pick', 'flag_pick', 'pick_allele', 'per_gene', 'pick_allele_gene', 'flag_pick_allele', 'flag_pick_allele_gene']}]
variants_to_table_fields			string[]
variants_to_table_genotype_fields			string[]
vep_to_table_fields			string[]
vep_plugins			string[]
sample_name			string
docm_vcf		Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)	File	['.tbi']
vep_custom_annotations		custom type, check types directory for input format	../types/vep_custom_annotation.yml#vep_custom_annotation[]
readcount_minimum_mapping_quality			int?
readcount_minimum_base_quality			int?

Outputs

Name	Label	Description	Type	Secondary Files
varscan_vcf			File	['.tbi']
docm_gatk_vcf			File
annotated_vcf			File	['.tbi']
final_vcf			File	['.tbi']
final_tsv			File
vep_summary			File
tumor_snv_bam_readcount_tsv			File
tumor_indel_bam_readcount_tsv			File

Steps

Name	CWL Run
varscan	subworkflows/varscan_germline.cwl
docm	subworkflows/docm_germline.cwl
combine_variants	tools/germline_combine_variants.cwl
decompose	tools/vt_decompose.cwl
annotate_variants	tools/vep.cwl
bam_readcount	tools/bam_readcount.cwl
add_bam_readcount_to_vcf	subworkflows/vcf_readcount_annotator.cwl
index	tools/index_vcf.cwl
hard_filter	tools/select_variants.cwl
af_filter	tools/filter_vcf_custom_allele_freq.cwl
coding_variant_filter	tools/filter_vcf_coding_variant.cwl
bgzip_filtered	tools/bgzip.cwl
index_filtered	tools/index_vcf.cwl
variants_to_table	tools/variants_to_table.cwl
add_vep_fields_to_table	tools/add_vep_fields_to_table.cwl