cwlVersion: v1.0 class: Workflow id: kfdrc-annofuse-wf requirements: - class: MultipleInputFeatureRequirement inputs: sample_name: { type: 'string', doc: "Sample name to apply. Ought to be one from some kind of clinical database" } FusionGenome: { type: 'File', doc: "Tar ball with fusion_annot_lib.idx and blast_pairs.idx from STAR-Fusion CTAT Genome lib", "sbg:suggestedValue": { class: 'File', path: '63cff818facdd82011c8d6fe', name: 'GRCh38_v39_fusion_annot_custom.tar.gz' } } genome_untar_path: { type: 'string?', doc: "This is what the path will be when genome_tar is unpackaged", default: "GRCh38_v39_CTAT_lib_Mar242022.CUSTOM" } rsem_expr_file: { type: 'File', doc: "gzipped rsem gene expression file" } arriba_output_file: { type: 'File', doc: "Output from arriba, usually extension arriba.fusions.tsv" } col_num: { type: 'int?', doc: "0-based column number in file of fusion name, use 24 for arriba v1.1, 30 for v2", default: 30 } star_fusion_output_file: { type: 'File', doc: "Output from STAR Fusion, usually extension STAR.fusion_predictions.abridged.coding_effect.tsv" } output_basename: { type: 'string', doc: "String to use as basename for outputs" } outputs: annofuse_filtered_fusions_tsv: { type: 'File?', outputSource: annoFuse_filter/filtered_fusions_tsv, doc: "Filtered output of formatted and annotated Star Fusion and arriba results" } steps: format_arriba_output: run: ../tools/format_arriba_fusion_file.cwl in: arriba_fusion_file: arriba_output_file sample_name: sample_name out: [formatted_fusion_tsv] annotate_arriba: run: ../tools/fusion_annotator.cwl in: input_fusion_file: format_arriba_output/formatted_fusion_tsv genome_tar: FusionGenome genome_untar_path: genome_untar_path col_num: col_num output_basename: output_basename out: [annotated_tsv] annoFuse_filter: run: ../tools/annoFuse.cwl in: arriba_formatted_fusions: annotate_arriba/annotated_tsv starfusion_formatted_fusions: star_fusion_output_file rsem_expr_file: rsem_expr_file sample_name: sample_name output_basename: output_basename out: [filtered_fusions_tsv] $namespaces: sbg: https://sevenbridges.com hints: - class: 'sbg:AWSInstanceType' value: c5.2xlarge;ebs-gp2;400 doc: "Chosen for speed and lower cost"