#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "wgs alignment and tumor-only 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] omni_vcf: type: File secondaryFiles: [.tbi] qc_intervals: type: File picard_metric_accumulation_level: type: string variant_detection_intervals: type: File 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? vep_pick: type: - "null" - type: enum symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"] sample_name: type: string docm_vcf: type: File vep_custom_annotations: type: ../types/vep_custom_annotation.yml#vep_custom_annotation[] doc: "custom type, check types directory for input format" readcount_minimum_mapping_quality: type: int? readcount_minimum_base_quality: type: int? 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[] 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 gc_bias_metrics: type: File outputSource: alignment_and_qc/gc_bias_metrics gc_bias_metrics_chart: type: File outputSource: alignment_and_qc/gc_bias_metrics_chart gc_bias_metrics_summary: type: File outputSource: alignment_and_qc/gc_bias_metrics_summary wgs_metrics: type: File outputSource: alignment_and_qc/wgs_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 varscan_vcf: type: File outputSource: detect_variants/varscan_vcf secondaryFiles: [.tbi] docm_gatk_vcf: type: File outputSource: detect_variants/docm_gatk_vcf annotated_vcf: type: File outputSource: detect_variants/annotated_vcf secondaryFiles: [.tbi] final_vcf: type: File outputSource: detect_variants/final_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 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 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 summary_hs_metrics: type: File[] outputSource: alignment_and_qc/summary_hs_metrics steps: alignment_and_qc: run: alignment_wgs.cwl in: reference: reference sequence: 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 minimum_mapping_quality: readcount_minimum_mapping_quality minimum_base_quality: readcount_minimum_base_quality per_base_intervals: per_base_intervals per_target_intervals: per_target_intervals summary_intervals: summary_intervals out: [bam, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary, wgs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics] detect_variants: run: tumor_only_detect_variants.cwl in: reference: reference bam: alignment_and_qc/bam interval_list: variant_detection_intervals #varscan_strand_filter: #varscan_min_coverage: #varscan_min_var_freq: #varscan_p_value: #varscan_min_reads: #maximum_population_allele_frequency: vep_cache_dir: vep_cache_dir synonyms_file: synonyms_file vep_pick: vep_pick vep_ensembl_assembly: vep_ensembl_assembly vep_ensembl_version: vep_ensembl_version vep_ensembl_species: vep_ensembl_species #variants_to_table_fields: #variants_to_table_genotype_fields: #vep_to_table_fields: sample_name: sample_name docm_vcf: docm_vcf vep_custom_annotations: vep_custom_annotations readcount_minimum_mapping_quality: readcount_minimum_mapping_quality readcount_minimum_base_quality: readcount_minimum_base_quality out: [varscan_vcf, docm_gatk_vcf, annotated_vcf, final_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_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]