manorm.cwl

cwlVersion: v1.0
class: Workflow


requirements:
  - class: StepInputExpressionRequirement
  - class: InlineJavascriptRequirement
  - class: MultipleInputFeatureRequirement


'sd:upstream':
  first_chipseq_sample:
    - "chipseq-se.cwl"
    - "chipseq-pe.cwl"
    - "trim-chipseq-pe.cwl"
    - "trim-chipseq-se.cwl"
  second_chipseq_sample:
    - "chipseq-se.cwl"
    - "chipseq-pe.cwl"
    - "trim-chipseq-pe.cwl"
    - "trim-chipseq-se.cwl"
  genome_indices:
    - "genome-indices.cwl"


inputs:

  alias:
    type: string
    label: "Experiment short name/Alias"
    sd:preview:
      position: 1

  peak_file_first:
    type: File
    format: "http://edamontology.org/format_3475"
    label: "ChIP-Seq sample one"
    doc: "TSV peak file, formatted as iaintersect output"
    'sd:upstreamSource': "first_chipseq_sample/iaintersect_result"
    'sd:localLabel': true

  peak_file_second:
    type: File
    format: "http://edamontology.org/format_3475"
    label: "ChIP-Seq sample two"
    doc: "TSV peak file, formatted as iaintersect output"
    'sd:upstreamSource': "second_chipseq_sample/iaintersect_result"
    'sd:localLabel': true

  bam_file_first:
    type: File
    format: "http://edamontology.org/format_2572"
    label: "First BAM file"
    doc: "BAM alignment file"
    'sd:upstreamSource': "first_chipseq_sample/bambai_pair"

  bam_file_second:
    type: File
    format: "http://edamontology.org/format_2572"
    label: "Second BAM file"
    doc: "BAM alignment file"
    'sd:upstreamSource': "second_chipseq_sample/bambai_pair"

  annotation_file:
    type: File
    label: "Annotation file"
    format: "http://edamontology.org/format_3475"
    doc: "Tab-separated annotation file"
    'sd:upstreamSource': "genome_indices/annotation"

  fragment_size_first:
    type: int?
    label: "First fragment size"
    doc: "Fragment size, int"
    default: 150
    'sd:layout':
      advanced: true

  fragment_size_second:
    type: int?
    label: "Second fragment size"
    doc: "Fragment size, int"
    default: 150
    'sd:layout':
      advanced: true

  output_filename:
    type: string?
    label: "MAnorm output TSV filename"
    doc: "MAnorm output TSV filename"
    default: "manorm_common_peak.tsv"
    'sd:layout':
      advanced: true

outputs:

  common_peak_file:
    type: File
    format: "http://edamontology.org/format_3475"
    label: "MAnorm common peak resutls, TSV"
    doc: "MAnorm generated list of common peaks with assigned genes"
    outputSource: restore_columns/restored_peak_file
    'sd:visualPlugins':
    - syncfusiongrid:
        Title: 'MAnorm Common Peak Results'


steps:

  manorm:
    in:
      peak_file_first: peak_file_first
      peak_file_second: peak_file_second
      bam_file_first: bam_file_first
      bam_file_second: bam_file_second
      fragment_size_first: fragment_size_first
      fragment_size_second: fragment_size_second
    out: [common_peak_file]
    run:
      cwlVersion: v1.0
      class: CommandLineTool
      requirements:
      - class: DockerRequirement
        dockerPull: biowardrobe2/manorm:v0.0.1
      inputs:
        peak_file_first:
          type: File
          inputBinding:
            position: 5
        peak_file_second:
          type: File
          inputBinding:
            position: 6
        bam_file_first:
          type: File
          inputBinding:
            position: 7
        bam_file_second:
          type: File
          inputBinding:
            position: 9
        fragment_size_first:
          type: int
          inputBinding:
            position: 10
        fragment_size_second:
          type: int
          inputBinding:
            position: 11
      outputs:
        common_peak_file:
          type: File
          outputBinding:
            glob: "MAnorm_result_commonPeak_merged.xls"
      baseCommand: ["run_manorm.sh"]

  filter_columns:
    in:
      peak_file: manorm/common_peak_file
      script:
        default: >
          cat $0 | grep -v "start" | awk
          'BEGIN {print "chr\tstart\tend\tlength\tabs_summit\tpileup\t-log10(pvalue)\tfold_enrichment\t-log10(qvalue)\tname"}
          {print $1"\t"$2"\t"$3"\t"$3-$2+1"\t0\t"NR"\t0\t0\t0\t0"}' > `basename $0`
    out: [filtered_peak_file]
    run:
      cwlVersion: v1.0
      class: CommandLineTool
      requirements:
      - class: DockerRequirement
        dockerPull: biowardrobe2/scidap:v0.0.3
      inputs:
        script:
          type: string
          inputBinding:
            position: 1
        peak_file:
          type: File
          inputBinding:
            position: 2
      outputs:
        filtered_peak_file:
          type: File
          outputBinding:
            glob: "*"
      baseCommand: [bash, '-c']

  assign_genes:
      in:
        peak_file: filter_columns/filtered_peak_file
        annotation_file: annotation_file
        output_filename: output_filename
        promoter_bp:
          default: 1000
      out: [peaks_and_genes_file]
      run:
        cwlVersion: v1.0
        class: CommandLineTool
        requirements:
        - class: DockerRequirement
          dockerPull: biowardrobe2/iaintersect:v0.0.2
        inputs:
          peak_file:
            type: File
            inputBinding:
              position: 1
              prefix: --in=
              separate: false
          annotation_file:
            type: File
            inputBinding:
              position: 2
              prefix: --a=
              separate: false
          output_filename:
            type: string
            inputBinding:
              position: 3
              prefix: --out=
              separate: false
          promoter_bp:
            type: int
            inputBinding:
              position: 4
              prefix: --promoter=
              separate: false
        outputs:
          peaks_and_genes_file:
            type: File
            outputBinding:
              glob: $(inputs.output_filename)
        baseCommand: [iaintersect]

  restore_columns:
    in:
      peak_files: [assign_genes/peaks_and_genes_file, manorm/common_peak_file]
      script:
        default: |
          cat $0 | grep -v "start" | sort -k 11n > sorted_iaintersect_result.tsv
          cat $1 | grep -v "start" > manorm_result.tsv
          echo -e "refseq_id\tgene_id\ttxStart\ttxEnd\tstrand\tchrom\tstart\tend\tlength\tregion\tdescription\t#raw_read_1\t#raw_read_2\tM_value_rescaled\tA_value_rescaled\t-log10(p-value)" > `basename $0`;
          cat sorted_iaintersect_result.tsv | paste - manorm_result.tsv | cut -f 1-9,15,19-24 >> `basename $0`
          rm sorted_iaintersect_result.tsv manorm_result.tsv
    out: [restored_peak_file]
    run:
      cwlVersion: v1.0
      class: CommandLineTool
      requirements:
      - class: DockerRequirement
        dockerPull: biowardrobe2/scidap:v0.0.3
      inputs:
        script:
          type: string
          inputBinding:
            position: 1
        peak_files:
          type: File[]
          inputBinding:
            position: 2
      outputs:
        restored_peak_file:
          type: File
          outputBinding:
            glob: "*"
      baseCommand: [bash, '-c']


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

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

s:name: "MAnorm - quantitative comparison of ChIP-Seq data"
label: "MAnorm - quantitative comparison of ChIP-Seq data"

s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/workflows/manorm.cwl
s:codeRepository: https://github.com/datirium/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:michael.kotliar@cchmc.org
          s:sameAs:
          - id: http://orcid.org/0000-0002-6486-3898

doc: |
  MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications.

s:about: |
  What is MAnorm?
  --------------

  MAnorm is a robust model for quantitative comparison of ChIP-Seq data sets of TFs (transcription factors) or epigenetic modifications and you can use it for:

  * Normalization of two ChIP-seq samples
  * Quantitative comparison (differential analysis) of two ChIP-seq samples
  * Evaluating the overlap enrichment of the protein binding sites(peaks)
  * Elucidating underlying mechanisms of cell-type specific gene regulation

  How MAnorm works?
  ----------------

  MAnorm uses common peaks of two samples as a reference to build the rescaling model for normalization, which is based on the empirical assumption that if a chromatin-associated protein has a substantial number of peaks shared in two conditions, the binding at these common regions will tend to be determined by similar mechanisms, and thus should exhibit similar global binding intensities across samples. The observed differences on common peaks are presumed to reflect the scaling relationship of ChIP-Seq signals between two samples, which can be applied to all peaks.