/
tumor_only_exome.cwl
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tumor_only_exome.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and tumor-only variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/trimming_options.yml
- $import: ../types/vep_custom_annotation.yml
- class: SubworkflowFeatureRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "sequence: sequencing data and readgroup information"
doc: |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying
readgroup information. Note that in the @RG field ID and SM are required.
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
bqsr_known_sites:
type: File[]
secondaryFiles: [.tbi]
doc: "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis."
bqsr_intervals:
type: string[]?
bait_intervals:
type: File
target_intervals:
type: File
label: "target_intervals: interval_list file of targets used in the sequencing experiment"
doc: |
target_intervals is an interval_list corresponding to the targets for the capture reagent.
Bed files with this information can be converted to interval_lists with Picard BedToIntervalList.
In general for a WES exome reagent bait_intervals and target_intervals are the same.
target_interval_padding:
type: int
label: "target_interval_padding: number of bp flanking each target region in which to allow variant calls"
doc: |
The effective coverage of capture products generally extends out beyond the actual regions
targeted. This parameter allows variants to be called in these wingspan regions, extending
this many base pairs from each side of the target regions.
default: 100
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
varscan_strand_filter:
type: int?
default: 0
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.1
varscan_p_value:
type: float?
default: 0.99
varscan_min_reads:
type: int?
default: 2
maximum_population_allele_frequency:
type: float?
default: 0.001
vep_cache_dir:
type:
- string
- Directory
vep_ensembl_assembly:
type: string
doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
vep_ensembl_version:
type: string
doc: "ensembl version - Must be present in the cache directory. Example: 95"
vep_ensembl_species:
type: string
doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
synonyms_file:
type: File?
annotate_coding_only:
type: boolean?
default: true
vep_pick:
type:
- "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:
type: string[]?
default: [CHROM,POS,REF,ALT,set]
variants_to_table_genotype_fields:
type: string[]?
default: [GT,AD,AF,DP]
vep_to_table_fields:
type: string[]?
default: [Consequence,SYMBOL,Feature_type,Feature,HGVSc,HGVSp,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,HGNC_ID,Existing_variation,gnomADe_AF,CLIN_SIG,SOMATIC,PHENO]
sample_name:
type: string
docm_vcf:
type: File
secondaryFiles: [.tbi]
vep_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
qc_minimum_mapping_quality:
type: int?
qc_minimum_base_quality:
type: int?
readcount_minimum_mapping_quality:
type: int?
readcount_minimum_base_quality:
type: int?
outputs:
cram:
type: File
outputSource: index_cram/indexed_cram
mark_duplicates_metrics:
type: File
outputSource: alignment_and_qc/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: alignment_and_qc/insert_size_metrics
insert_size_histogram:
type: File
outputSource: alignment_and_qc/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: alignment_and_qc/alignment_summary_metrics
hs_metrics:
type: File
outputSource: alignment_and_qc/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: alignment_and_qc/summary_hs_metrics
flagstats:
type: File
outputSource: alignment_and_qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: alignment_and_qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: alignment_and_qc/verify_bam_id_depth
varscan_vcf:
type: File
outputSource: detect_variants/varscan_vcf
secondaryFiles: [.tbi]
docm_gatk_vcf:
type: File
outputSource: detect_variants/docm_gatk_vcf
annotated_vcf:
type: File
outputSource: detect_variants/annotated_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: detect_variants/final_vcf
secondaryFiles: [.tbi]
final_tsv:
type: File
outputSource: detect_variants/final_tsv
vep_summary:
type: File
outputSource: detect_variants/vep_summary
tumor_snv_bam_readcount_tsv:
type: File
outputSource: detect_variants/tumor_snv_bam_readcount_tsv
tumor_indel_bam_readcount_tsv:
type: File
outputSource: detect_variants/tumor_indel_bam_readcount_tsv
steps:
alignment_and_qc:
run: alignment_exome.cwl
in:
reference: reference
sequence: sequence
trimming: trimming
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
omni_vcf: omni_vcf
picard_metric_accumulation_level: picard_metric_accumulation_level
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
out:
[bam, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
pad_target_intervals:
run: ../tools/interval_list_expand.cwl
in:
interval_list: target_intervals
roi_padding: target_interval_padding
out:
[expanded_interval_list]
detect_variants:
run: tumor_only_detect_variants.cwl
in:
reference: reference
bam: alignment_and_qc/bam
roi_intervals: pad_target_intervals/expanded_interval_list
varscan_strand_filter: varscan_strand_filter
varscan_min_coverage: varscan_min_coverage
varscan_min_var_freq: varscan_min_var_freq
varscan_p_value: varscan_p_value
varscan_min_reads: varscan_min_reads
maximum_population_allele_frequency: maximum_population_allele_frequency
vep_cache_dir: vep_cache_dir
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
synonyms_file: synonyms_file
vep_pick: vep_pick
variants_to_table_fields: variants_to_table_fields
variants_to_table_genotype_fields: variants_to_table_genotype_fields
vep_to_table_fields: vep_to_table_fields
sample_name: sample_name
docm_vcf: docm_vcf
vep_custom_annotations: vep_custom_annotations
readcount_minimum_mapping_quality: readcount_minimum_mapping_quality
readcount_minimum_base_quality: readcount_minimum_base_quality
out:
[varscan_vcf, docm_gatk_vcf, annotated_vcf, final_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv]
bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: alignment_and_qc/bam
reference: reference
out:
[cram]
index_cram:
run: ../tools/index_cram.cwl
in:
cram: bam_to_cram/cram
out:
[indexed_cram]