#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "gathered exome alignment and somatic variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.yml
- $import: ../types/vep_custom_annotation.yml
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
tumor_sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "tumor_sequence: MT sequencing data and readgroup information"
doc: |
tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with
accompanying readgroup information. Note that in the @RG field ID and SM are required.
tumor_cram_name:
type: string?
default: 'tumor.cram'
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "normal_sequence: WT sequencing data and readgroup information"
doc: |
normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with
accompanying readgroup information. Note that in the @RG field ID and SM are required.
normal_cram_name:
type: string?
default: 'normal.cram'
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"
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
qc_minimum_mapping_quality:
type: int?
default: 0
qc_minimum_base_quality:
type: int?
default: 0
strelka_cpu_reserved:
type: int?
default: 8
scatter_count:
type: int
doc: "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs"
mutect_artifact_detection_mode:
type: boolean
mutect_max_alt_allele_in_normal_fraction:
type: float?
mutect_max_alt_alleles_in_normal_count:
type: int?
varscan_strand_filter:
type: int?
default: 0
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.05
varscan_p_value:
type: float?
default: 0.99
varscan_max_normal_freq:
type: float?
pindel_insert_size:
type: int
default: 400
docm_vcf:
type: File
secondaryFiles: [.tbi]
doc: "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)"
filter_docm_variants:
type: boolean?
default: true
doc: "Determines whether variants found only via genotyping of DOCM sites will be filtered (as DOCM_ONLY) or passed through as variant calls"
filter_somatic_llr_threshold:
type: float
default: 5
doc: "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure."
filter_somatic_llr_tumor_purity:
type: float
default: 1
doc: "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1"
filter_somatic_llr_normal_contamination_rate:
type: float
default: 0
doc: "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1"
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?
hgvs_annotation:
type: boolean?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
cle_vcf_filter:
type: boolean
default: false
variants_to_table_fields:
type: string[]
default: [CHROM,POS,ID,REF,ALT,set,AC,AF]
variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
vep_to_table_fields:
type: string[]
default: [HGVSc,HGVSp]
vep_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
output_dir:
type: string
somalier_vcf:
type: File
tumor_sample_name:
type: string
normal_sample_name:
type: string
validated_variants:
type: File?
secondaryFiles: [.tbi]
doc: "An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main output VCF"
outputs:
final_outputs:
type: string[]
outputSource: gatherer/gathered_files
steps:
somatic_exome:
run: somatic_exome.cwl
in:
reference: reference
tumor_sequence: tumor_sequence
tumor_cram_name: tumor_cram_name
normal_sequence: normal_sequence
normal_cram_name: normal_cram_name
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
bait_intervals: bait_intervals
target_intervals: target_intervals
target_interval_padding: target_interval_padding
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
strelka_cpu_reserved: strelka_cpu_reserved
scatter_count: scatter_count
mutect_artifact_detection_mode: mutect_artifact_detection_mode
mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_count
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_max_normal_freq: varscan_max_normal_freq
pindel_insert_size: pindel_insert_size
docm_vcf: docm_vcf
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
annotate_coding_only: annotate_coding_only
hgvs_annotation: hgvs_annotation
vep_pick: vep_pick
cle_vcf_filter: cle_vcf_filter
filter_somatic_llr_threshold: filter_somatic_llr_threshold
filter_somatic_llr_tumor_purity: filter_somatic_llr_tumor_purity
filter_somatic_llr_normal_contamination_rate: filter_somatic_llr_normal_contamination_rate
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
vep_custom_annotations: vep_custom_annotations
somalier_vcf: somalier_vcf
tumor_sample_name: tumor_sample_name
normal_sample_name: normal_sample_name
validated_variants: validated_variants
out:
[tumor_cram, tumor_mark_duplicates_metrics, tumor_insert_size_metrics, tumor_alignment_summary_metrics, tumor_hs_metrics, tumor_per_target_coverage_metrics, tumor_per_base_coverage_metrics, tumor_per_base_hs_metrics, tumor_summary_hs_metrics, tumor_flagstats, tumor_verify_bam_id_metrics, tumor_verify_bam_id_depth, normal_cram, normal_mark_duplicates_metrics, normal_insert_size_metrics, normal_alignment_summary_metrics, normal_hs_metrics, normal_per_target_coverage_metrics, normal_per_target_hs_metrics, normal_per_base_coverage_metrics, normal_per_base_hs_metrics, normal_summary_hs_metrics, normal_flagstats, normal_verify_bam_id_metrics, normal_verify_bam_id_depth, mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_filtered_vcf, pindel_unfiltered_vcf, pindel_filtered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv, somalier_concordance_metrics, somalier_concordance_statistics]
gatherer:
run: ../tools/gatherer.cwl
in:
output_dir: output_dir
all_files:
source: [somatic_exome/tumor_cram, somatic_exome/tumor_mark_duplicates_metrics, somatic_exome/tumor_insert_size_metrics, somatic_exome/tumor_alignment_summary_metrics, somatic_exome/tumor_hs_metrics, somatic_exome/tumor_per_target_coverage_metrics, somatic_exome/tumor_per_base_coverage_metrics, somatic_exome/tumor_per_base_hs_metrics, somatic_exome/tumor_summary_hs_metrics, somatic_exome/tumor_flagstats, somatic_exome/tumor_verify_bam_id_metrics, somatic_exome/tumor_verify_bam_id_depth, somatic_exome/normal_cram, somatic_exome/normal_mark_duplicates_metrics, somatic_exome/normal_insert_size_metrics, somatic_exome/normal_alignment_summary_metrics, somatic_exome/normal_hs_metrics, somatic_exome/normal_per_target_coverage_metrics, somatic_exome/normal_per_target_hs_metrics, somatic_exome/normal_per_base_coverage_metrics, somatic_exome/normal_per_base_hs_metrics, somatic_exome/normal_summary_hs_metrics, somatic_exome/normal_flagstats, somatic_exome/normal_verify_bam_id_metrics, somatic_exome/normal_verify_bam_id_depth, somatic_exome/mutect_unfiltered_vcf, somatic_exome/mutect_filtered_vcf, somatic_exome/strelka_unfiltered_vcf, somatic_exome/strelka_filtered_vcf, somatic_exome/varscan_unfiltered_vcf, somatic_exome/varscan_filtered_vcf, somatic_exome/pindel_unfiltered_vcf, somatic_exome/pindel_filtered_vcf, somatic_exome/docm_filtered_vcf, somatic_exome/final_vcf, somatic_exome/final_filtered_vcf, somatic_exome/final_tsv, somatic_exome/vep_summary, somatic_exome/tumor_snv_bam_readcount_tsv, somatic_exome/tumor_indel_bam_readcount_tsv, somatic_exome/normal_snv_bam_readcount_tsv, somatic_exome/normal_indel_bam_readcount_tsv]
valueFrom: ${
function flatten(inArr, outArr) {
var arrLen = inArr.length;
for (var i = 0; i < arrLen; i++) {
if (Array.isArray(inArr[i])) {
flatten(inArr[i], outArr);
}
else {
outArr.push(inArr[i]);
}
}
return outArr;
}
var no_secondaries = flatten(self, []);
var all_files = [];
var arrLen = no_secondaries.length;
for (var i = 0; i < arrLen; i++) {
all_files.push(no_secondaries[i]);
var secondaryLen = no_secondaries[i].secondaryFiles.length;
for (var j = 0; j < secondaryLen; j++) {
all_files.push(no_secondaries[i].secondaryFiles[j]);
}
}
return all_files;
}
out: [gathered_files]