path: root/workflow/phases.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
$namespaces:
  dc: http://purl.org/dc/elements/1.1/
  license: https://spdx.org/licenses/

inputs:
  annotated_markdown: File

outputs:
  annotated_html:
    type: File
    outputSource: phase3_convert_to_html/html_with_rdfa
  annotated_pdf:
    type: File
    outputSource: phase3_convert_to_pdf/latex_with_xmp
  markdown_with_metadata:
    type: File
    outputSource: phase2_extract/markdown
  plain_markdown:
    type: File
    outputSource: phase1_strip/markdown

steps:
  phase3_convert_to_html:
    in:
      input_file: annotated_markdown
      output_format:
        default: html
    run: pandoc-filter-tool.cwl
    out:
    - html_with_rdfa
    - latex_with_xmp
  phase3_convert_to_pdf:
    in:
      input_file: annotated_markdown
      output_format:
        default: pdf
    run: pandoc-filter-tool.cwl
    out:
    - html_with_rdfa
    - latex_with_xmp
  phase2_extract:
    in:
      input_file: annotated_markdown
      output_format:
        default: commonmark
    run: pandoc-filter-tool.cwl
    out:
    - markdown
  phase1_strip:
    in:
      input_file: annotated_markdown
      output_format:
        default: commonmark
    run: pandoc-filter-tool.cwl
    out:
    - markdown
dc:license: license:GPL-3.0-or-later
dc:rights: Copyright 2025, Jonas Smedegaard <dr@jones.dk>