#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: ScatterFeatureRequirement inputs: input_mirna: File input_mrna: File input_coords: 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: output: type: File outputSource: concatenate_results/output steps: calculate_mirza: run: calculate_MIRZA.cwl scatter: coords in: seq: input_mrna motifs: input_mirna coords: input_coords tree: input_tree msa: input_multiple_alignments threshold: settings_mirza_threshold out: [ output ] calculate_contrafold: run: calculate_contrafold.cwl scatter: coords in: seq: input_mrna coords: input_coords contextLen_L: settings_contextLen_L out: [ output ] calculate_flanks: run: calculate_flanks_composition.cwl scatter: coords in: seq: input_mrna coords: input_coords out: [ output ] calculate_distance: run: calculate_distance.cwl scatter: coords in: seq: input_mrna coords: input_coords out: [ output ] merge_results_add_probability_and_calculate_per_gene_score: run: merge_results_add_probability_and_calculate_per_gene_score.cwl scatter: [ coords, mirza, contrafold, flanks, distance ] scatterMethod: dotproduct in: coords: input_coords mirza: calculate_mirza/output contrafold: calculate_contrafold/output flanks: calculate_flanks/output distance: calculate_distance/output model_bls: input_model_with_bls model_nobls: input_model_without_bls split_by: settings_split_by column: settings_index_after_split out: [ output ] concatenate_results: run: concatenate.cwl in: files: merge_results_add_probability_and_calculate_per_gene_score/output output_file: output_file_name out: [ output ]