#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "exome alignment and germline variant detection" requirements: - class: SchemaDefRequirement types: - $import: ../types/labelled_file.yml - $import: ../types/sequence_data.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[] 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 emit_reference_confidence: type: type: enum symbols: ['NONE', 'BP_RESOLUTION', 'GVCF'] gvcf_gq_bands: type: string[] intervals: type: type: array items: type: array items: string 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" vep_plugins: type: string[]? doc: "array of plugins to use when running vep" synonyms_file: type: File? annotate_coding_only: type: boolean? qc_minimum_mapping_quality: type: int? qc_minimum_base_quality: type: int? vep_custom_annotations: type: ../types/vep_custom_annotation.yml#vep_custom_annotation[] doc: "custom type, check types directory for input format" variants_to_table_fields: type: string[]? variants_to_table_genotype_fields: type: string[]? vep_to_table_fields: type: string[]? 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 gvcf: type: File[] outputSource: detect_variants/gvcf final_vcf: type: File outputSource: detect_variants/final_vcf secondaryFiles: [.tbi] filtered_vcf: type: File outputSource: detect_variants/filtered_vcf secondaryFiles: [.tbi] vep_summary: type: File outputSource: detect_variants/vep_summary final_tsv: type: File outputSource: detect_variants/final_tsv filtered_tsv: type: File outputSource: detect_variants/filtered_tsv steps: alignment_and_qc: run: alignment_exome.cwl in: reference: reference sequence: sequence 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 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] 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 annotate_coding_only: annotate_coding_only limit_variant_intervals: target_intervals vep_ensembl_assembly: vep_ensembl_assembly vep_ensembl_version: vep_ensembl_version vep_ensembl_species: vep_ensembl_species vep_plugins: vep_plugins vep_to_table_fields: vep_to_table_fields vep_custom_annotations: vep_custom_annotations variants_to_table_fields: variants_to_table_fields variants_to_table_genotype_fields: variants_to_table_genotype_fields out: [gvcf, final_vcf, filtered_vcf, vep_summary, final_tsv, filtered_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]