#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: ScatterFeatureRequirement - class: SubworkflowFeatureRequirement inputs: input_mirna: File input_mrna: File input_tree: File input_multiple_alignments: File input_model_with_bls: File input_model_without_bls: File output_file_name: string settings_split_by: string settings_index_after_split: int settings_mirza_threshold: float settings_contextLen_L: int settings_contextLen_U: int outputs: mirzag_output: type: File outputSource: analyze/output steps: prepare_mirnas: run: tools/prepare_mirnas.cwl in: input: input_mirna out: [ output ] generate_mrna_chunks: run: tools/generate_mrna_chunks.cwl in: input: input_mrna out: [ output ] mirna_expressions: run: tools/generate_mirna_expressions.cwl in: input: input_mirna out: [ output ] mirza: run: tools/mirza.cwl scatter: [ mrna, mirna ] scatterMethod: flat_crossproduct in: expressions: mirna_expressions/output mrna: generate_mrna_chunks/output mirna: prepare_mirnas/output out: [ output ] mirza_parser: run: tools/extract_data_from_mirza_output.cwl scatter: [ mirza ] in: mirza: mirza/output mrna: input_mrna out: [ output ] concatenate_mirza: run: tools/concatenate.cwl in: files: mirza_parser/output output_file: default: "mirza_scan_results" out: [ output ] filter_duplicates_from_scan: run: tools/filter_duplicates_from_scan.cwl in: coords: concatenate_mirza/output out: [ output ] split: run: tools/split_mirza_results.cwl in: file: filter_duplicates_from_scan/output out: [ output ] analyze: run: tools/analysis.cwl in: input_mirna: input_mirna input_mrna: input_mrna input_coords: source: split/output input_tree: input_tree input_multiple_alignments: input_multiple_alignments input_model_with_bls: input_model_with_bls input_model_without_bls: input_model_without_bls output_file_name: output_file_name settings_split_by: settings_split_by settings_index_after_split: settings_index_after_split settings_mirza_threshold: settings_mirza_threshold settings_contextLen_L: settings_contextLen_L settings_contextLen_U: settings_contextLen_U out: [ output ]