#!/usr/bin/env cwl-runner

cwlVersion: v1.1
class: Workflow
doc: "Workflow to go from YAML (metadata) + FASTA (sequence) to TTL (metadata)"

inputs:
  path-fasta:
    type: string
    doc: input FASTA to validate

  format_to_check:
    type: string
    default: text/fasta

  path-yaml:
    type: string
    doc: input YAML to validate and convert in TTL

steps:
  check_format:
    in:
      path_fasta: path-fasta
      format_to_check: format_to_check
    doc: the input has to be a valid FASTA format file
    out: []
    run: check_format.cwl

  check_sequence:
    in:
      path_fasta: path-fasta
    doc: the input sequence has to be enough similar to the reference
    out: []
    run: check_sequence.cwl

  check_metadata:
    in:
      path_yaml: path-yaml
      path_fasta: path-fasta
    doc: check the input metadata information to put in the knowledge graph
    out: []
    run: check_metadata.cwl

outputs: []