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pipelines_detect_variants_wgs.cwl

Travis CI User edited this page Mar 16, 2020 · 23 revisions

Documentation for detect_variants_wgs.cwl

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Overview

Detect Variants workflow for WGS pipeline

Inputs

Name Label Description Type Secondary Files
reference string
tumor_bam File ['.bai', '^.bai']
normal_bam File ['.bai', '^.bai']
interval_list File
strelka_exome_mode boolean
strelka_cpu_reserved int?
readcount_minimum_base_quality int?
readcount_minimum_mapping_quality int?
mutect_scatter_count int?
varscan_strand_filter int?
varscan_min_coverage int?
varscan_min_var_freq float?
varscan_p_value float?
varscan_max_normal_freq float?
pindel_insert_size int
docm_vcf File ['.tbi']
filter_docm_variants boolean?
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']}]
vep_plugins string[]?
filter_gnomADe_maximum_population_allele_frequency float?
filter_mapq0_threshold float?
filter_minimum_depth int?
cle_vcf_filter boolean?
filter_somatic_llr_threshold float?
variants_to_table_fields string[]?
variants_to_table_genotype_fields string[]?
vep_to_table_fields string[]?
tumor_sample_name string
normal_sample_name string
vep_custom_annotations custom type, check types directory for input format ../types/vep_custom_annotation.yml#vep_custom_annotation[]
known_variants Previously discovered variants to be flagged in this pipelines's output vcf File? ['.tbi']

Outputs

Name Label Description Type Secondary Files
mutect_unfiltered_vcf File ['.tbi']
mutect_filtered_vcf File ['.tbi']
strelka_unfiltered_vcf File ['.tbi']
strelka_filtered_vcf File ['.tbi']
varscan_unfiltered_vcf File ['.tbi']
varscan_filtered_vcf File ['.tbi']
docm_filtered_vcf File ['.tbi']
final_vcf File ['.tbi']
final_filtered_vcf File ['.tbi']
final_tsv File
vep_summary File
tumor_snv_bam_readcount_tsv File
tumor_indel_bam_readcount_tsv File
normal_snv_bam_readcount_tsv File
normal_indel_bam_readcount_tsv File

Steps

Name CWL Run
mutect subworkflows/mutect.cwl
strelka subworkflows/strelka_and_post_processing.cwl
varscan subworkflows/varscan_pre_and_post_processing.cwl
docm subworkflows/docm_cle.cwl
combine tools/combine_variants_wgs.cwl
add_docm_variants tools/docm_add_variants.cwl
decompose tools/vt_decompose.cwl
decompose_index tools/index_vcf.cwl
annotate_variants tools/vep.cwl
tumor_bam_readcount tools/bam_readcount.cwl
normal_bam_readcount tools/bam_readcount.cwl
add_tumor_bam_readcount_to_vcf subworkflows/vcf_readcount_annotator.cwl
add_normal_bam_readcount_to_vcf subworkflows/vcf_readcount_annotator.cwl
index tools/index_vcf.cwl
filter_vcf subworkflows/filter_vcf.cwl
annotated_filter_bgzip tools/bgzip.cwl
annotated_filter_index tools/index_vcf.cwl
variants_to_table tools/variants_to_table.cwl
add_vep_fields_to_table tools/add_vep_fields_to_table.cwl
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