pipelines_detect_variants_nonhuman.cwl

Documentation for detect_variants_nonhuman.cwl

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Overview

Detect Variants workflow

Inputs

Name	Label	Description	Type	Secondary Files
reference			['string', 'File']	['.fai', '^.dict']
tumor_bam			File	['.bai', '^.bai']
normal_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
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
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_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

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']
pindel_unfiltered_vcf			File	['.tbi']
pindel_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
pindel	subworkflows/pindel.cwl
combine	tools/combine_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_nonhuman.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