subworkflows_joint_genotype.cwl
Travis CI User edited this page Feb 24, 2021
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joint genotyping for trios or small cohorts
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| reference | ['string', 'File'] | ['.fai', '^.dict'] | ||
| gvcfs | File[] | |||
| intervals | intervals used to parallelize genotyping. Example: chr1],[chr2],[chr3],[chr4,chr5 | {'type': 'array', 'items': {'type': 'array', 'items': 'string'}} | ||
| 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 | ||
| vep_plugins | 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[] | ||
| roi_intervals | region of interest interval list file, used to limit called variants in final filtered output files | File | ||
| variants_to_table_fields | string[]? | |||
| variants_to_table_genotype_fields | string[]? | |||
| vep_to_table_fields | string[]? | |||
| final_tsv_prefix | string? | |||
| filter_gnomAD_maximum_population_allele_frequency | float |
| Name | Label | Description | Type | Secondary Files |
|---|---|---|---|---|
| raw_vcf | File | ['.tbi'] | ||
| final_vcf | File | ['.tbi'] | ||
| filtered_vcf | File | ['.tbi'] | ||
| vep_summary | File | |||
| final_tsv | File | |||
| filtered_tsv | File |
| Name | CWL Run |
|---|---|
| combine_gvcfs | tools/combine_gvcfs.cwl |
| genotype_gvcf | tools/gatk_genotypegvcfs.cwl |
| merge_vcfs | tools/picard_merge_vcfs.cwl |
| annotate_variants | tools/vep.cwl |
| bgzip_index_annotated_vcf | subworkflows/bgzip_and_index.cwl |
| filter_vcf | subworkflows/germline_filter_vcf.cwl |
| filtered_variants_to_table | tools/variants_to_table.cwl |
| filtered_add_vep_fields_to_table | tools/add_vep_fields_to_table.cwl |
| set_filtered_tsv_name | tools/staged_rename.cwl |
| final_variants_to_table | tools/variants_to_table.cwl |
| final_add_vep_fields_to_table | tools/add_vep_fields_to_table.cwl |
| set_final_tsv_name | tools/staged_rename.cwl |