cwlVersion: v1.0
class: Workflow
label: EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

requirements:
 - class: SubworkflowFeatureRequirement
 - class: SchemaDefRequirement
   types: 
    - $import: ../tools/FragGeneScan-model.yaml
    - $import: ../tools/trimmomatic-sliding_window.yaml
    - $import: ../tools/trimmomatic-end_mode.yaml
    - $import: ../tools/trimmomatic-phred.yaml

inputs:
  forward_reads:
    type: File
    format: edam:format_1930  # FASTQ
  reverse_reads:
    type: File
    format: edam:format_1930  # FASTQ

outputs:
  processed_sequences:
    type: File
    outputSource: convert_trimmed-reads_to_fasta/fasta

steps:
  overlap_reads:
    label: Paired-end overlapping reads are merged
    run: ../tools/seqprep.cwl
    in:
      forward_reads: forward_reads
      reverse_reads: reverse_reads
    out: [ merged_reads, forward_unmerged_reads, reverse_unmerged_reads ]

  combine_overlaped_and_unmerged_reads:
    run: ../tools/seqprep-merge.cwl
    in: 
      merged_reads: overlap_reads/merged_reads
      forward_unmerged_reads: overlap_reads/forward_unmerged_reads
      reverse_unmerged_reads: overlap_reads/reverse_unmerged_reads
    out: [ merged_with_unmerged_reads ]

  trim_quality_control:
    doc: |
      Low quality trimming (low quality ends and sequences with < quality scores
      less than 15 over a 4 nucleotide wide window are removed)
    run: ../tools/trimmomatic.cwl
    in:
      reads1: combine_overlaped_and_unmerged_reads/merged_with_unmerged_reads
      phred: { default: '33' }
      leading: { default: 3 }
      trailing: { default: 3 }
      end_mode: { default: SE }
      minlen: { default: 100 }
      slidingwindow:
        default:
          windowSize: 4
          requiredQuality: 15
    out: [reads1_trimmed]

  convert_trimmed-reads_to_fasta:
    run: ../tools/fastq_to_fasta.cwl
    in:
      fastq: trim_quality_control/reads1_trimmed
    out: [ fasta ]

$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"