#!/usr/bin/env cwl-runner cwlVersion: v1.1 class: CommandLineTool doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)" inputs: path_fasta: type: File inputBinding: position: 1 path_yaml: type: File inputBinding: position: 2 steps: check_format: in: {path_fasta: path_fasta, path_valid_formats: '../../bh20sequploader/validation/formats', format_to_check: 'text/fasta'} #out: true/false or nothing and it has to block the execution if the format is wrong run: check_format.cwl check_metadata: # input and output # run: check_metadata.cwl check_header: # id_fasta has to be equal to id_yaml # run: check_header.cwl check_sequence: # The sequence has to be similar to the reference # run: check_sequence.cwl