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germline_wgs.cwl
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germline_wgs.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "wgs alignment and germline variant detection"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- class: SubworkflowFeatureRequirement
inputs:
reference: string
bams:
type: File[]
readgroups:
type: string[]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
emit_reference_confidence:
type: string
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
qc_intervals:
type: File
variant_reporting_intervals:
type: File
vep_cache_dir:
type: string
synonyms_file:
type: File?
coding_only:
type: boolean?
custom_gnomad_vcf:
type: File?
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]?
minimum_mapping_quality:
type: int?
minimum_base_quality:
type: int?
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[]
custom_clinvar_vcf:
type: File?
secondaryFiles: [.tbi]
cnvkit_diagram:
type: boolean?
cnvkit_drop_low_coverage:
type: boolean?
cnvkit_method:
type: string?
cnvkit_reference_cnn:
type: File
cnvkit_scatter_plot:
type: boolean?
cnvkit_male_reference:
type: boolean?
cnvkit_vcf_name:
type: string?
manta_call_regions:
type: File?
manta_non_wgs:
type: boolean?
manta_output_contigs:
type: boolean?
smoove_exclude_regions:
type: File?
outputs:
cram:
type: File
outputSource: alignment_and_qc/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
gc_bias_metrics:
type: File
outputSource: alignment_and_qc/gc_bias_metrics
gc_bias_metrics_chart:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_chart
gc_bias_metrics_summary:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_summary
wgs_metrics:
type: File
outputSource: alignment_and_qc/wgs_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
gvcf:
type: File[]
outputSource: detect_variants/gvcf
final_vcf:
type: File
outputSource: detect_variants/final_vcf
secondaryFiles: [.tbi]
coding_vcf:
type: File
outputSource: detect_variants/coding_vcf
secondaryFiles: [.tbi]
limited_vcf:
type: File
outputSource: detect_variants/limited_vcf
secondaryFiles: [.tbi]
vep_summary:
type: File
outputSource: detect_variants/vep_summary
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
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
summary_hs_metrics:
type: File[]
outputSource: alignment_and_qc/summary_hs_metrics
bamcoverage_bigwig:
type: File
outputSource: alignment_and_qc/bamcoverage_bigwig
cn_diagram:
type: File?
outputSource: variant_callers/cn_diagram
cn_scatter_plot:
type: File?
outputSource: variant_callers/cn_scatter_plot
tumor_antitarget_coverage:
type: File
outputSource: variant_callers/tumor_antitarget_coverage
tumor_target_coverage:
type: File
outputSource: variant_callers/tumor_target_coverage
tumor_bin_level_ratios:
type: File
outputSource: variant_callers/tumor_bin_level_ratios
tumor_segmented_ratios:
type: File
outputSource: variant_callers/tumor_segmented_ratios
cnvkit_vcf:
type: File
outputSource: variant_callers/cnvkit_vcf
manta_diploid_variants:
type: File?
outputSource: variant_callers/manta_diploid_variants
manta_somatic_variants:
type: File?
outputSource: variant_callers/manta_somatic_variants
manta_all_candidates:
type: File
outputSource: variant_callers/manta_all_candidates
manta_small_candidates:
type: File
outputSource: variant_callers/manta_small_candidates
manta_tumor_only_variants:
type: File?
outputSource: variant_callers/manta_tumor_only_variants
smoove_output_variants:
type: File
outputSource: variant_callers/smoove_output_variants
steps:
alignment_and_qc:
run: wgs_alignment.cwl
in:
reference: reference
bams: bams
readgroups: readgroups
mills: mills
known_indels: known_indels
dbsnp_vcf: dbsnp_vcf
omni_vcf: omni_vcf
intervals: qc_intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
bqsr_intervals: bqsr_intervals
minimum_mapping_quality: minimum_mapping_quality
minimum_base_quality: minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
out:
[cram, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary, wgs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics, bamcoverage_bigwig]
extract_freemix:
in:
verify_bam_id_metrics: alignment_and_qc/verify_bam_id_metrics
out:
[freemix_score]
run:
class: ExpressionTool
requirements:
- class: InlineJavascriptRequirement
inputs:
verify_bam_id_metrics:
type: File
inputBinding:
loadContents: true
outputs:
freemix_score:
type: string?
expression: |
${
var metrics = inputs.verify_bam_id_metrics.contents.split("\n");
if ( metrics[0].split("\t")[6] == 'FREEMIX' ) {
return {'freemix_score': metrics[1].split("\t")[6]};
} else {
return {'freemix_score:': null };
}
}
detect_variants:
run: ../subworkflows/germline_detect_variants.cwl
in:
reference: reference
cram: alignment_and_qc/cram
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
contamination_fraction: extract_freemix/freemix_score
vep_cache_dir: vep_cache_dir
synonyms_file: synonyms_file
coding_only: coding_only
custom_gnomad_vcf: custom_gnomad_vcf
limit_variant_intervals: variant_reporting_intervals
custom_clinvar_vcf: custom_clinvar_vcf
out:
[gvcf, final_vcf, coding_vcf, limited_vcf, vep_summary]
variant_callers:
run: ../subworkflows/single_sample_sv_callers.cwl
in:
cram: alignment_and_qc/cram
reference: reference
cnvkit_diagram: cnvkit_diagram
cnvkit_drop_low_coverage: cnvkit_drop_low_coverage
cnvkit_method: cnvkit_method
cnvkit_reference_cnn: cnvkit_reference_cnn
cnvkit_scatter_plot: cnvkit_scatter_plot
cnvkit_male_reference: cnvkit_male_reference
cnvkit_vcf_name: cnvkit_vcf_name
manta_call_regions: manta_call_regions
manta_non_wgs: manta_non_wgs
manta_output_contigs: manta_output_contigs
smoove_exclude_regions: smoove_exclude_regions
out:
[cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios, cnvkit_vcf, manta_diploid_variants, manta_somatic_variants, manta_all_candidates, manta_small_candidates, manta_tumor_only_variants, smoove_output_variants]