heatmap.cwl

cwlVersion: v1.0
class: Workflow


requirements:
  - class: InlineJavascriptRequirement
  - class: SubworkflowFeatureRequirement


inputs:

  bam_file:
    type: File[]
    label: "BAM files"
    format: "http://edamontology.org/format_2572"
    doc: "Array of input BAM files"

  genelist_file:
    type: File
    label: "Genelist file"
    format: "http://edamontology.org/format_3475"
    doc: "Genelist file"

  fragment_size:
    type: int[]
    label: "Fragment sizes"
    doc: "Array of fragment sizes"

  total_reads:
    type: int[]
    label: "Total reads numbers"
    doc: "Array of total reads number for downstream normalization"

#  genebody_hist_filename:
#    type: string
#    label: "Genebody histogram file name"
#    doc: "Genebody histogram file name"

  threads:
    type: int?
    default: 1
    label: "Number of threads"
    doc: "Number of threads for those steps that support multithreading"


outputs:

  heatmap_file:
    type: File[]
    label: "TSS centered refactored homer generated heatmap JSON files"
    format: "http://edamontology.org/format_3464"
    doc: "Heatmap JSON files generated by Homer annotatePeaks.pl with TSS centered peak file"
    outputSource: split_heatmap/refactored_heatmap_file

#  genebody_hist_file:
#    type: File
#    label: "Homer gene body histogram file"
#    format: "http://edamontology.org/format_3475"
#    doc: "Genebody histogram file generated by Homer makeMetaGeneProfile.pl"
#    outputSource: make_genebody_hist/histogram_file


steps:

  make_tag_folders:
    run: ../subworkflows/heatmap-prepare.cwl
    in:
      bam_file: bam_file
      fragment_size: fragment_size
      total_reads: total_reads
    out: [tag_folder]

  center_genelist_on_tss:
    run: ../tools/custom-bash.cwl
    in:
      input_file: genelist_file
      script:
        default: cat "$0" | grep -v "refseq_id" | awk '{tss=$4; if ($6 == "-") tss=$5; print NR"\t"$3"\t"tss"\t"tss"\t"$6}' > `basename $0`
    out: [output_file]

#  make_peak_file:
#    run: ../tools/custom-bash.cwl
#    in:
#      input_file: genelist_file
#      script:
#        default: cat "$0" | grep -v "refseq_id" | awk '{print NR"\t"$3"\t"$4"\t"$5"\t"$6}' > `basename $0`
#    out: [output_file]

  make_tss_heatmap:
    run: ../tools/homer-annotate-peaks-hist.cwl
    in:
      peak_file: center_genelist_on_tss/output_file
      tag_folders: make_tag_folders/tag_folder
      hist_width:
        default: 10000
      hist_bin_size:
        default: 50
      export_heatmap:
        default: True
      threads: threads
      histogram_filename:
        default: "default.tsv"
    out: [histogram_file]

  split_heatmap:
    run: ../tools/split-heatmap.cwl
    in:
      heatmap_file: make_tss_heatmap/histogram_file
      output_filename: bam_file
    out: [refactored_heatmap_file]

#  make_genebody_hist:
#    run: ../tools/homer-make-metagene-profile.cwl
#    in:
#      peak_file: make_peak_file/output_file
#      tag_folders: make_tag_folders/tag_folder
#      flank_width:
#        default: 5000
#      flank_bin_size:
#        default: 50
#      genebody_bin_count:
#        default: 1000
#      threads: threads
#      histogram_filename: genebody_hist_filename
#    out: [histogram_file]


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

$schemas:
- http://schema.org/docs/schema_org_rdfa.html

s:name: "heatmap"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/workflows/heatmap.cwl
s:codeRepository: https://github.com/Barski-lab/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0

s:isPartOf:
  class: s:CreativeWork
  s:name: Common Workflow Language
  s:url: http://commonwl.org/

s:creator:
- class: s:Organization
  s:legalName: "Cincinnati Children's Hospital Medical Center"
  s:location:
  - class: s:PostalAddress
    s:addressCountry: "USA"
    s:addressLocality: "Cincinnati"
    s:addressRegion: "OH"
    s:postalCode: "45229"
    s:streetAddress: "3333 Burnet Ave"
    s:telephone: "+1(513)636-4200"
  s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
  s:department:
  - class: s:Organization
    s:legalName: "Allergy and Immunology"
    s:department:
    - class: s:Organization
      s:legalName: "Barski Research Lab"
      s:member:
      - class: s:Person
        s:name: Michael Kotliar
        s:email: mailto:misha.kotliar@gmail.com
        s:sameAs:
        - id: http://orcid.org/0000-0002-6486-3898
      - class: s:Person
        s:name: Andrey Kartashov
        s:email: mailto:Andrey.Kartashov@cchmc.org
        s:sameAs:
        - id: http://orcid.org/0000-0001-9102-5681

doc: |
  Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file.
  Returns array of heatmap JSON files with the names that have the same basenames as input BAM files,
  but with .json extension

s:about: |
  Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file.
  Returns array of heatmap JSON files with the names that have the same basenames as input BAM files,
  but with .json extension