#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow

inputs:
  - id: sequences
    type: File
  - id: reads
    type: File[]
  - id: base_count
    type: int
  - id: output_dest
    type: string
  - id: coverage_report_src
    type: File?
    default: coverage_calculation/coverage_report.py


outputs:
  - id: bwa_index
    type: File
    outputSource: bwa_index/output
  - id: bwa_mem
    type: File
    outputSource: bwa_mem/output
  - id: samtools_view
    type: File
    outputSource: samtools_view/output
  - id: samtools_sort
    type: File
    outputSource: samtools_sort/sorted
  - id: samtools_index
    type: File
    outputSource: samtools_index/alignments_with_index
  - id: metabat_coverage
    type: File
    outputSource: metabat_jgi/output
  - id: logfile
    type: File
    outputSource: coverage_report/logfile

steps:
  - id: bwa_index
    run: ./bwa-index.cwl
    in:
      - id: sequences
        source: sequences
    out:
      - id: output

  - id: bwa_mem
    run: ./bwa-mem.cwl
    in:
      - id: reads
        source:
          - reads
      - id: reference
        source: bwa_index/output
    out:
      - id: output

  - id: samtools_view
    run: ./samtools-view.cwl
    in:
      - id: input
        source: bwa_mem/output
      - id: uncompressed
        default: true
      - id: unselected_output_reads
        default: true
      - id: output_name
        default: "unsorted.bam"
    out:
      - id: output

  - id: samtools_sort
    run: ./samtools-sort.cwl
    in:
      - id: input
        source: samtools_view/output
      - id: output_name
        default: "sorted.bam"
    out:
      - id: sorted

  - id: samtools_index
    run: ./samtools-index.cwl
    in:
      - id: alignments
        source: samtools_sort/sorted
    out:
      - id: alignments_with_index

  - id: metabat_jgi
    run: ./metabat-jgi-summarise.cwl
    in:
      - id: input
        source: samtools_index/alignments_with_index
      - id: outputDepth
        default: "coverage.tab"
    out:
      - id: output
  - id: coverage_report
    run: ./coverage-report.cwl
    in:
      - id: base_count
        source: base_count
      - id: src
        source: coverage_report_src
      - id: output
        source: output_dest
      - id: coverage_file
        source: metabat_jgi/output
    out:
      - id: logfile



$namespaces:
 edam: http://edamontology.org/
 s: http://schema.org/

$schemas:
 - http://edamontology.org/EDAM_1.16.owl
 - https://schema.org/docs/schema_org_rdfa.html

s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute"