#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "exome alignment and somatic variant detection for cle purpose" 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_name: type: string? default: 'tumor' normal_bams: type: File[] normal_readgroups: type: string[] 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[] 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 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 filter_minimum_depth: type: int? default: 20 vep_cache_dir: type: string 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] custom_gnomad_vcf: type: File? secondaryFiles: [.tbi] custom_clinvar_vcf: type: File? secondaryFiles: [.tbi] somalier_vcf: type: File outputs: 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_hs_metrics: type: File outputSource: tumor_alignment_and_qc/hs_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 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_hs_metrics: type: File outputSource: normal_alignment_and_qc/hs_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 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] pindel_unfiltered_vcf: type: File outputSource: detect_variants/pindel_unfiltered_vcf secondaryFiles: [.tbi] pindel_filtered_vcf: type: File outputSource: detect_variants/pindel_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 somalier_concordance_metrics: type: File outputSource: concordance/somalier_pairs somalier_concordance_statistics: type: File outputSource: concordance/somalier_samples steps: tumor_alignment_and_qc: run: exome_alignment.cwl in: reference: reference bams: tumor_bams readgroups: tumor_readgroups 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 minimum_mapping_quality: qc_minimum_mapping_quality minimum_base_quality: qc_minimum_base_quality final_name: source: tumor_name valueFrom: "$(self).bam" out: [bam, mark_duplicates_metrics, insert_size_metrics, 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] normal_alignment_and_qc: run: exome_alignment.cwl in: reference: reference bams: normal_bams readgroups: normal_readgroups 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 minimum_mapping_quality: qc_minimum_mapping_quality minimum_base_quality: qc_minimum_base_quality final_name: source: normal_name valueFrom: "$(self).bam" out: [bam, mark_duplicates_metrics, insert_size_metrics, 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] 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.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: true 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 filter_minimum_depth: filter_minimum_depth 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 custom_gnomad_vcf: custom_gnomad_vcf custom_clinvar_vcf: custom_clinvar_vcf out: [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] 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]