#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "exome alignment and somatic variant detection" requirements: - class: SubworkflowFeatureRequirement inputs: reference: string tumor_bams: type: File[] tumor_readgroups: type: string[] normal_bams: type: File[] normal_readgroups: type: string[] 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_target_intervals: type: File per_target_bait_intervals: type: File per_base_intervals: type: File per_base_bait_intervals: type: 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 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] vep_cache_dir: type: string? synonyms_file: type: File? annotate_coding_only: type: boolean? hgvs_annotation: type: boolean? 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] outputs: tumor_cram: type: File outputSource: tumor_alignment_and_qc/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_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_alignment_and_qc/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_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_unfiltered_vcf: type: File outputSource: detect_variants/docm_unfiltered_vcf 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_bam_readcount_tsv: type: File outputSource: detect_variants/tumor_bam_readcount_tsv normal_bam_readcount_tsv: type: File outputSource: detect_variants/normal_bam_readcount_tsv 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_target_intervals: per_target_intervals per_target_bait_intervals: per_target_bait_intervals per_base_intervals: per_base_intervals per_base_bait_intervals: per_base_bait_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 out: [cram, 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, 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_target_intervals: per_target_intervals per_target_bait_intervals: per_target_bait_intervals per_base_intervals: per_base_intervals per_base_bait_intervals: per_base_bait_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 out: [cram, 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, flagstats, verify_bam_id_metrics, verify_bam_id_depth] detect_variants: run: detect_variants/detect_variants.cwl in: reference: reference tumor_cram: tumor_alignment_and_qc/cram normal_cram: normal_alignment_and_qc/cram 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 vep_cache_dir: vep_cache_dir synonyms_file: synonyms_file annotate_coding_only: annotate_coding_only hgvs_annotation: hgvs_annotation 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 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_unfiltered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_bam_readcount_tsv, normal_bam_readcount_tsv]