#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "gathered exome 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: type: - string - File secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa] tumor_sequence: type: ../types/sequence_data.yml#sequence_data[] tumor_cram_name: type: string? default: 'tumor.cram' normal_sequence: type: ../types/sequence_data.yml#sequence_data[] normal_cram_name: type: string? default: 'normal.cram' 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 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? 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? hgvs_annotation: 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" output_dir: type: string 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: final_outputs: type: string[] outputSource: gatherer/gathered_files steps: somatic_exome: run: somatic_exome.cwl in: reference: reference tumor_sequence: tumor_sequence tumor_cram_name: tumor_cram_name normal_sequence: normal_sequence normal_cram_name: normal_cram_name 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 interval_list: interval_list cosmic_vcf: cosmic_vcf panel_of_normals_vcf: panel_of_normals_vcf 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 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 hgvs_annotation: hgvs_annotation 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 vep_custom_annotations: vep_custom_annotations somalier_vcf: somalier_vcf tumor_sample_name: tumor_sample_name normal_sample_name: normal_sample_name known_variants: known_variants out: [tumor_cram, tumor_mark_duplicates_metrics, tumor_insert_size_metrics, tumor_alignment_summary_metrics, tumor_hs_metrics, tumor_per_target_coverage_metrics, tumor_per_base_coverage_metrics, tumor_per_base_hs_metrics, tumor_summary_hs_metrics, tumor_flagstats, tumor_verify_bam_id_metrics, tumor_verify_bam_id_depth, normal_cram, normal_mark_duplicates_metrics, normal_insert_size_metrics, normal_alignment_summary_metrics, normal_hs_metrics, normal_per_target_coverage_metrics, normal_per_target_hs_metrics, normal_per_base_coverage_metrics, normal_per_base_hs_metrics, normal_summary_hs_metrics, normal_flagstats, normal_verify_bam_id_metrics, normal_verify_bam_id_depth, 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, somalier_concordance_metrics, somalier_concordance_statistics] gatherer: run: ../tools/gatherer.cwl in: output_dir: output_dir all_files: source: [somatic_exome/tumor_cram, somatic_exome/tumor_mark_duplicates_metrics, somatic_exome/tumor_insert_size_metrics, somatic_exome/tumor_alignment_summary_metrics, somatic_exome/tumor_hs_metrics, somatic_exome/tumor_per_target_coverage_metrics, somatic_exome/tumor_per_base_coverage_metrics, somatic_exome/tumor_per_base_hs_metrics, somatic_exome/tumor_summary_hs_metrics, somatic_exome/tumor_flagstats, somatic_exome/tumor_verify_bam_id_metrics, somatic_exome/tumor_verify_bam_id_depth, somatic_exome/normal_cram, somatic_exome/normal_mark_duplicates_metrics, somatic_exome/normal_insert_size_metrics, somatic_exome/normal_alignment_summary_metrics, somatic_exome/normal_hs_metrics, somatic_exome/normal_per_target_coverage_metrics, somatic_exome/normal_per_target_hs_metrics, somatic_exome/normal_per_base_coverage_metrics, somatic_exome/normal_per_base_hs_metrics, somatic_exome/normal_summary_hs_metrics, somatic_exome/normal_flagstats, somatic_exome/normal_verify_bam_id_metrics, somatic_exome/normal_verify_bam_id_depth, somatic_exome/mutect_unfiltered_vcf, somatic_exome/mutect_filtered_vcf, somatic_exome/strelka_unfiltered_vcf, somatic_exome/strelka_filtered_vcf, somatic_exome/varscan_unfiltered_vcf, somatic_exome/varscan_filtered_vcf, somatic_exome/pindel_unfiltered_vcf, somatic_exome/pindel_filtered_vcf, somatic_exome/docm_filtered_vcf, somatic_exome/final_vcf, somatic_exome/final_filtered_vcf, somatic_exome/final_tsv, somatic_exome/vep_summary, somatic_exome/tumor_snv_bam_readcount_tsv, somatic_exome/tumor_indel_bam_readcount_tsv, somatic_exome/normal_snv_bam_readcount_tsv, somatic_exome/normal_indel_bam_readcount_tsv] valueFrom: ${ function flatten(inArr, outArr) { var arrLen = inArr.length; for (var i = 0; i < arrLen; i++) { if (Array.isArray(inArr[i])) { flatten(inArr[i], outArr); } else { outArr.push(inArr[i]); } } return outArr; } var no_secondaries = flatten(self, []); var all_files = []; var arrLen = no_secondaries.length; for (var i = 0; i < arrLen; i++) { all_files.push(no_secondaries[i]); var secondaryLen = no_secondaries[i].secondaryFiles.length; for (var j = 0; j < secondaryLen; j++) { all_files.push(no_secondaries[i].secondaryFiles[j]); } } return all_files; } out: [gathered_files]