#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Whole genome 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: string tumor_sequence: type: ../types/sequence_data.yml#sequence_data[] tumor_name: type: string? default: 'tumor' normal_sequence: type: ../types/sequence_data.yml#sequence_data[] normal_name: type: string? default: 'normal' mills: type: File secondaryFiles: [.tbi] known_indels: type: File secondaryFiles: [.tbi] dbsnp_vcf: type: File secondaryFiles: [.tbi] bqsr_intervals: type: string[] target_intervals: type: File per_base_intervals: type: ../types/labelled_file.yml#labelled_file[] per_target_intervals: type: ../types/labelled_file.yml#labelled_file[] qc_intervals: type: 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 default: false 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 - 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? 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" manta_call_regions: type: File? secondaryFiles: [.tbi] manta_non_wgs: type: boolean? default: false manta_output_contigs: type: boolean? somalier_vcf: type: File tumor_sample_name: type: string normal_sample_name: type: string known_variants: type: File? secondaryFiles: [.tbi] doc: "Previously discovered variants to be flagged in this pipelines's output vcf" outputs: ##tumor alignment and QC tumor_cram: type: File outputSource: tumor_index_cram/indexed_cram tumor_mark_duplicates_metrics: type: File outputSource: tumor_alignment_and_qc/mark_duplicates_metrics tumor_insert_size_metrics: type: File outputSource: tumor_alignment_and_qc/insert_size_metrics tumor_alignment_summary_metrics: type: File outputSource: tumor_alignment_and_qc/alignment_summary_metrics tumor_per_target_coverage_metrics: type: File[] outputSource: tumor_alignment_and_qc/per_target_coverage_metrics tumor_per_target_hs_metrics: type: File[] outputSource: tumor_alignment_and_qc/per_target_hs_metrics tumor_per_base_coverage_metrics: type: File[] outputSource: tumor_alignment_and_qc/per_base_coverage_metrics tumor_per_base_hs_metrics: type: File[] outputSource: tumor_alignment_and_qc/per_base_hs_metrics tumor_summary_hs_metrics: type: File[] outputSource: tumor_alignment_and_qc/summary_hs_metrics tumor_flagstats: type: File outputSource: tumor_alignment_and_qc/flagstats tumor_verify_bam_id_metrics: type: File outputSource: tumor_alignment_and_qc/verify_bam_id_metrics tumor_verify_bam_id_depth: type: File outputSource: tumor_alignment_and_qc/verify_bam_id_depth tumor_insert_size_histogram: type: File outputSource: tumor_alignment_and_qc/insert_size_histogram tumor_gc_bias_metrics: type: File outputSource: tumor_alignment_and_qc/gc_bias_metrics tumor_gc_bias_metrics_chart: type: File outputSource: tumor_alignment_and_qc/gc_bias_metrics_chart tumor_gc_bias_metrics_summary: type: File outputSource: tumor_alignment_and_qc/gc_bias_metrics_summary tumor_wgs_metrics: type: File outputSource: tumor_alignment_and_qc/wgs_metrics ##normal alignment and qc normal_cram: type: File outputSource: normal_index_cram/indexed_cram normal_mark_duplicates_metrics: type: File outputSource: normal_alignment_and_qc/mark_duplicates_metrics normal_insert_size_metrics: type: File outputSource: normal_alignment_and_qc/insert_size_metrics normal_alignment_summary_metrics: type: File outputSource: normal_alignment_and_qc/alignment_summary_metrics normal_per_target_coverage_metrics: type: File[] outputSource: normal_alignment_and_qc/per_target_coverage_metrics normal_per_target_hs_metrics: type: File[] outputSource: normal_alignment_and_qc/per_target_hs_metrics normal_per_base_coverage_metrics: type: File[] outputSource: normal_alignment_and_qc/per_base_coverage_metrics normal_per_base_hs_metrics: type: File[] outputSource: normal_alignment_and_qc/per_base_hs_metrics normal_summary_hs_metrics: type: File[] outputSource: normal_alignment_and_qc/summary_hs_metrics normal_flagstats: type: File outputSource: normal_alignment_and_qc/flagstats normal_verify_bam_id_metrics: type: File outputSource: normal_alignment_and_qc/verify_bam_id_metrics normal_verify_bam_id_depth: type: File outputSource: normal_alignment_and_qc/verify_bam_id_depth normal_insert_size_histogram: type: File outputSource: normal_alignment_and_qc/insert_size_histogram normal_gc_bias_metrics: type: File outputSource: normal_alignment_and_qc/gc_bias_metrics normal_gc_bias_metrics_chart: type: File outputSource: normal_alignment_and_qc/gc_bias_metrics_chart normal_gc_bias_metrics_summary: type: File outputSource: normal_alignment_and_qc/gc_bias_metrics_summary normal_wgs_metrics: type: File outputSource: normal_alignment_and_qc/wgs_metrics ##variant calling mutect_unfiltered_vcf: type: File outputSource: detect_variants/mutect_unfiltered_vcf secondaryFiles: [.tbi] mutect_filtered_vcf: type: File outputSource: detect_variants/mutect_filtered_vcf secondaryFiles: [.tbi] strelka_unfiltered_vcf: type: File outputSource: detect_variants/strelka_unfiltered_vcf secondaryFiles: [.tbi] strelka_filtered_vcf: type: File outputSource: detect_variants/strelka_filtered_vcf secondaryFiles: [.tbi] varscan_unfiltered_vcf: type: File outputSource: detect_variants/varscan_unfiltered_vcf secondaryFiles: [.tbi] varscan_filtered_vcf: type: File outputSource: detect_variants/varscan_filtered_vcf secondaryFiles: [.tbi] docm_filtered_vcf: type: File outputSource: detect_variants/docm_filtered_vcf secondaryFiles: [.tbi] final_vcf: type: File outputSource: detect_variants/final_vcf secondaryFiles: [.tbi] final_filtered_vcf: type: File outputSource: detect_variants/final_filtered_vcf secondaryFiles: [.tbi] final_tsv: type: File outputSource: detect_variants/final_tsv vep_summary: type: File outputSource: detect_variants/vep_summary tumor_snv_bam_readcount_tsv: type: File outputSource: detect_variants/tumor_snv_bam_readcount_tsv tumor_indel_bam_readcount_tsv: type: File outputSource: detect_variants/tumor_indel_bam_readcount_tsv normal_snv_bam_readcount_tsv: type: File outputSource: detect_variants/normal_snv_bam_readcount_tsv normal_indel_bam_readcount_tsv: type: File outputSource: detect_variants/normal_indel_bam_readcount_tsv diploid_variants: type: File? outputSource: manta/diploid_variants secondaryFiles: [.tbi] somatic_variants: type: File? outputSource: manta/somatic_variants secondaryFiles: [.tbi] all_candidates: type: File outputSource: manta/all_candidates secondaryFiles: [.tbi] small_candidates: type: File outputSource: manta/small_candidates secondaryFiles: [.tbi] tumor_only_variants: type: File? outputSource: manta/tumor_only_variants secondaryFiles: [.tbi] ##sample concordance check somalier_concordance_metrics: type: File outputSource: concordance/somalier_pairs somalier_concordance_statistics: type: File outputSource: concordance/somalier_samples steps: tumor_alignment_and_qc: run: alignment_wgs.cwl in: reference: reference sequence: tumor_sequence 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: qc_minimum_mapping_quality minimum_base_quality: qc_minimum_base_quality per_base_intervals: per_base_intervals per_target_intervals: per_target_intervals summary_intervals: summary_intervals sample_name: tumor_name out: [alignment_summary_metrics, bam, flagstats, gc_bias_metrics_chart, gc_bias_metrics_summary, gc_bias_metrics, insert_size_histogram, insert_size_metrics, mark_duplicates_metrics, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics, verify_bam_id_depth, verify_bam_id_metrics, wgs_metrics] normal_alignment_and_qc: run: alignment_wgs.cwl in: reference: reference sequence: normal_sequence 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: qc_minimum_mapping_quality minimum_base_quality: qc_minimum_base_quality per_base_intervals: per_base_intervals per_target_intervals: per_target_intervals summary_intervals: summary_intervals sample_name: normal_name out: [alignment_summary_metrics, bam, flagstats, gc_bias_metrics_chart, gc_bias_metrics_summary, gc_bias_metrics, insert_size_histogram, insert_size_metrics, mark_duplicates_metrics, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics, verify_bam_id_depth, verify_bam_id_metrics, wgs_metrics] concordance: run: ../tools/concordance.cwl in: reference: reference bam_1: tumor_alignment_and_qc/bam bam_2: normal_alignment_and_qc/bam vcf: somalier_vcf out: [somalier_pairs, somalier_samples] detect_variants: run: detect_variants_wgs.cwl in: reference: reference tumor_bam: tumor_alignment_and_qc/bam normal_bam: normal_alignment_and_qc/bam interval_list: interval_list dbsnp_vcf: dbsnp_vcf cosmic_vcf: cosmic_vcf panel_of_normals_vcf: panel_of_normals_vcf strelka_exome_mode: default: false 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 filter_docm_variants: filter_docm_variants 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 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 tumor_sample_name: tumor_sample_name normal_sample_name: normal_sample_name vep_custom_annotations: vep_custom_annotations known_variants: known_variants out: [mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_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] manta: run: ../tools/manta_somatic.cwl in: normal_bam: normal_alignment_and_qc/bam tumor_bam: tumor_alignment_and_qc/bam reference: reference non_wgs: manta_non_wgs output_contigs: manta_output_contigs out: [diploid_variants, somatic_variants, all_candidates, small_candidates, tumor_only_variants] tumor_bam_to_cram: run: ../tools/bam_to_cram.cwl in: bam: tumor_alignment_and_qc/bam reference: reference out: [cram] tumor_index_cram: run: ../tools/index_cram.cwl in: cram: tumor_bam_to_cram/cram out: [indexed_cram] normal_bam_to_cram: run: ../tools/bam_to_cram.cwl in: bam: normal_alignment_and_qc/bam reference: reference out: [cram] normal_index_cram: run: ../tools/index_cram.cwl in: cram: normal_bam_to_cram/cram out: [indexed_cram]