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gathered_somatic_exome.cwl
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gathered_somatic_exome.cwl
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#!/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
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
reference: string
tumor_bams:
type: File[]
tumor_readgroups:
type: string[]
tumor_cram_name:
type: string?
default: 'tumor.cram'
normal_bams:
type: File[]
normal_readgroups:
type: string[]
normal_cram_name:
type: string?
default: 'normal.cram'
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]
bait_intervals:
type: File
target_intervals:
type: File
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
interval_list:
type: File
cosmic_vcf:
type: File?
secondaryFiles: [.tbi]
panel_of_normals_vcf:
type: File?
secondaryFiles: [.tbi]
strelka_cpu_reserved:
type: int?
default: 8
mutect_scatter_count:
type: int
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]
filter_docm_variants:
type: boolean?
default: true
vep_cache_dir:
type: string?
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]
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
output_dir:
type: string
vep_assembly:
type: string
doc: Used to explicitly define which assembly version to use; required if there are two or more in the same directory
somalier_vcf:
type: File
outputs:
final_outputs:
type: string[]
outputSource: gatherer/gathered_files
steps:
somatic_exome:
run: somatic_exome.cwl
in:
reference: reference
tumor_bams: tumor_bams
tumor_readgroups: tumor_readgroups
tumor_cram_name: tumor_cram_name
normal_bams: normal_bams
normal_readgroups: normal_readgroups
normal_cram_name: normal_cram_name
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
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
interval_list: interval_list
cosmic_vcf: cosmic_vcf
panel_of_normals_vcf: panel_of_normals_vcf
strelka_cpu_reserved: strelka_cpu_reserved
mutect_scatter_count: mutect_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
synonyms_file: synonyms_file
annotate_coding_only: annotate_coding_only
hgvs_annotation: hgvs_annotation
vep_pick: vep_pick
cle_vcf_filter: cle_vcf_filter
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
custom_gnomad_vcf: custom_gnomad_vcf
vep_assembly: vep_assembly
somalier_vcf: somalier_vcf
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]