#!/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? secondaryFiles: [.tbi] manta_non_wgs: type: boolean? manta_output_contigs: type: boolean? smoove_exclude_regions: type: File? 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 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: [bam, 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 bam: alignment_and_qc/bam 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: bam: alignment_and_qc/bam 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] 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]