cwlVersion: v1.0
class: Workflow

requirements:
  - class: SubworkflowFeatureRequirement
  - class: InlineJavascriptRequirement
  - class: StepInputExpressionRequirement

inputs:
  - id: input_cram
    type: File
  - id: ref_fasta_files
    type: File[]

steps:
  - id: samtools_seq_cache_populate
    run: ../tools/samtools_seq_cache_populate.cwl
    in:
      ref_fasta_files: ref_fasta_files
    out: [ref_cache]
    hints:
      ResourceRequirement:
        ramMin: 100000
        coresMin: 1
        tmpdirMin: 1000

  - id: samtools_fastaref
    run: ../tools/samtools/samtools-fastaref.cwl
    in:
      ref_path_dir: samtools_seq_cache_populate/ref_cache
      output_file_name:
        default: "reference.fa"
      input: input_cram
    out: [reference_fasta]
    hints:
      ResourceRequirement:
        ramMin: 8000
        coresMin: 1
        tmpdirMin: 1000

  - id: samtools_faidx
    run: ../tools/samtools/samtools-faidx.cwl
    in:
      fasta: samtools_fastaref/reference_fasta
    out: [fasta_index]

  - id: samtools_dict
    run: ../tools/samtools/samtools-dict.cwl
    in:
      output:
        default: "reference.dict"
      fasta: samtools_fastaref/reference_fasta
    out: [fasta_dict]

  - id: combine_reference_files
    in:
      main_file: samtools_fastaref/reference_fasta
      secondary_files:
        - samtools_faidx/fasta_index
        - samtools_dict/fasta_dict
    out:
      [file_with_secondary_files]
    run: ../expression-tools/combine_files.cwl

outputs:
  - id: reference_fasta
    type: File
    outputSource: combine_reference_files/file_with_secondary_files
  - id: reference_dict
    type: File
    outputSource: samtools_dict/fasta_dict