#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow label: "Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs" requirements: - class: SubworkflowFeatureRequirement - class: StepInputExpressionRequirement inputs: detect_variants_vcf: type: File sample_name: type: string? default: 'TUMOR' normal_sample_name: type: string? default: 'NORMAL' rnaseq_bam: type: File secondaryFiles: ['.bai'] reference_fasta: type: - string - File secondaryFiles: [.fai, ^.dict] readcount_minimum_base_quality: type: int? readcount_minimum_mapping_quality: type: int? gene_expression_file: type: File transcript_expression_file: type: File expression_tool: type: string? default: 'kallisto' alleles: type: string[] prediction_algorithms: type: string[] epitope_lengths: type: int[]? binding_threshold: type: int? allele_specific_binding_thresholds: type: boolean? minimum_fold_change: type: float? peptide_sequence_length: type: int? top_score_metric: type: - "null" - type: enum symbols: ["lowest", "median"] additional_report_columns: type: - "null" - type: enum symbols: ["sample_name"] fasta_size: type: int? downstream_sequence_length: type: string? exclude_nas: type: boolean? phased_proximal_variants_vcf: type: File? secondaryFiles: ['.tbi'] maximum_transcript_support_level: type: - "null" - type: enum symbols: ["1", "2", "3", "4", "5"] normal_cov: type: int? tdna_cov: type: int? trna_cov: type: int? normal_vaf: type: float? tdna_vaf: type: float? trna_vaf: type: float? expn_val: type: float? net_chop_method: type: - "null" - type: enum symbols: ["cterm", "20s"] net_chop_threshold: type: float? netmhc_stab: type: boolean? n_threads: type: int? variants_to_table_fields: type: string[]? default: [CHROM,POS,ID,REF,ALT] variants_to_table_genotype_fields: type: string[]? default: [GT,AD,AF,DP,RAD,RAF,RDP,GX,TX] vep_to_table_fields: type: string[]? default: [HGVSc,HGVSp] outputs: annotated_vcf: type: File outputSource: add_transcript_expression_data_to_vcf/annotated_expression_vcf annotated_tsv: type: File outputSource: add_vep_fields_to_table/annotated_variants_tsv pvacseq_predictions: type: Directory outputSource: pvacseq/pvacseq_predictions steps: tumor_rna_bam_readcount: run: bam_readcount.cwl in: vcf: detect_variants_vcf sample: sample_name reference_fasta: reference_fasta bam: rnaseq_bam min_base_quality: readcount_minimum_base_quality min_mapping_quality: readcount_minimum_mapping_quality out: [snv_bam_readcount_tsv, indel_bam_readcount_tsv, normalized_vcf] add_tumor_rna_bam_readcount_to_vcf: run: vcf_readcount_annotator.cwl in: vcf: tumor_rna_bam_readcount/normalized_vcf snv_bam_readcount_tsv: tumor_rna_bam_readcount/snv_bam_readcount_tsv indel_bam_readcount_tsv: tumor_rna_bam_readcount/indel_bam_readcount_tsv data_type: default: 'RNA' sample_name: sample_name out: [annotated_bam_readcount_vcf] add_gene_expression_data_to_vcf: run: ../tools/vcf_expression_annotator.cwl in: vcf: add_tumor_rna_bam_readcount_to_vcf/annotated_bam_readcount_vcf expression_file: gene_expression_file expression_tool: expression_tool data_type: default: 'gene' sample_name: sample_name out: [annotated_expression_vcf] add_transcript_expression_data_to_vcf: run: ../tools/vcf_expression_annotator.cwl in: vcf: add_gene_expression_data_to_vcf/annotated_expression_vcf expression_file: transcript_expression_file expression_tool: expression_tool data_type: default: 'transcript' sample_name: sample_name out: [annotated_expression_vcf] index: run: ../tools/index_vcf.cwl in: vcf: add_transcript_expression_data_to_vcf/annotated_expression_vcf out: [indexed_vcf] pvacseq: run: ../tools/pvacseq.cwl in: input_vcf: index/indexed_vcf sample_name: sample_name alleles: alleles prediction_algorithms: prediction_algorithms epitope_lengths: epitope_lengths normal_sample_name: normal_sample_name minimum_fold_change: minimum_fold_change peptide_sequence_length: peptide_sequence_length top_score_metric: top_score_metric additional_report_columns: additional_report_columns fasta_size: fasta_size downstream_sequence_length: downstream_sequence_length exclude_nas: exclude_nas phased_proximal_variants_vcf: phased_proximal_variants_vcf maximum_transcript_support_level: maximum_transcript_support_level normal_cov: normal_cov tdna_cov: tdna_cov trna_cov: trna_cov normal_vaf: normal_vaf tdna_vaf: tdna_vaf trna_vaf: trna_vaf expn_val: expn_val net_chop_method: net_chop_method net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab n_threads: n_threads out: [pvacseq_predictions] variants_to_table: run: ../tools/variants_to_table.cwl in: reference: reference_fasta vcf: index/indexed_vcf fields: variants_to_table_fields genotype_fields: variants_to_table_genotype_fields out: [variants_tsv] add_vep_fields_to_table: run: ../tools/add_vep_fields_to_table.cwl in: vcf: index/indexed_vcf vep_fields: vep_to_table_fields tsv: variants_to_table/variants_tsv prefix: default: 'pvacseq' out: [annotated_variants_tsv]