cellbrowser-build-cellranger.cwl

cwlVersion: v1.0
class: CommandLineTool


hints:
- class: DockerRequirement
  dockerPull: biowardrobe2/cellbrowser:v0.0.2


requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entryname: cellbrowser.conf
    entry: |
      name = "cellbrowser"
      shortLabel="cellbrowser"
      priority = 1
      geneIdType="auto"
      exprMatrix="exprMatrix.tsv.gz"
      meta="meta.csv"
      coords=[
          {
              "file": "tsne.coords.csv",
              "shortLabel": "CellRanger t-SNE"
          },
          {
              "file": "umap.coords.csv",
              "shortLabel": "CellRanger UMAP"
          }
      ]
      markers=[
        {
          "file":"markers.tsv",
          "shortLabel":"Cluster-specific genes"
        }
      ]
      enumFields = ["Barcode"]
      clusterField="Cluster"
      labelField="Cluster"
  - entryname: desc.conf
    entry: |
      title = "CellBrowser"
      abstract = ""
      methods = ""
      biorxiv_url = ""
      custom = {}


inputs:

  bash_script:
    type: string?
    default: |
      #!/bin/bash
      echo "Prepare input data"
      mkdir -p ./cellbrowser_input/analysis ./cellbrowser_input/filtered_feature_bc_matrix
      cp -r $0/* ./cellbrowser_input/analysis/
      cp -r $1/* ./cellbrowser_input/filtered_feature_bc_matrix/
      echo "Run cbImportCellranger"
      cbImportCellranger -i cellbrowser_input -o cellbrowser_output --name cellbrowser
      cd ./cellbrowser_output
      echo "Copy UMAP coordinates files"
      cp ../cellbrowser_input/analysis/umap/2_components/projection.csv umap.coords.csv
      echo "Replace configuration files"
      rm -f cellbrowser.conf desc.conf
      cp ../cellbrowser.conf .
      cp ../desc.conf .
      if [[ -n $2 ]]; then
        echo "Aggregation metadata file was provided. Adding initial cell identity classes"
        cat $2 | grep -v "library_id" | awk '{print NR","$0}' > aggregation_metadata.csv
        cat meta.csv | grep -v "Barcode" > meta_headerless.csv
        echo "Barcode,Cluster,Identity" > meta.csv
        awk -F, 'NR==FNR {identity[$1]=$2; next} {split($1,barcode,"-"); print $0","identity[barcode[2]]}' aggregation_metadata.csv meta_headerless.csv >> meta.csv
        rm -f aggregation_metadata.csv meta_headerless.csv
      fi
      echo "Run cbBuild"
      cbBuild -o html_data
    inputBinding:
      position: 5
    doc: |
      Bash script to run cbImportCellranger and cbBuild commands

  secondary_analysis_report_folder:
    type: Directory
    inputBinding:
      position: 6
    doc: |
      Folder with secondary analysis results including dimensionality reduction,
      cell clustering, and differential expression produced by Cellranger Count
      or Cellranger Aggr

  filtered_feature_bc_matrix_folder:
    type: Directory
    inputBinding:
      position: 7
    doc: |
      Folder with filtered feature-barcode matrices containing only cellular
      barcodes in MEX format produced by Cellranger Count or Cellranger Aggr

  aggregation_metadata:
    type: File?
    inputBinding:
      position: 8
    doc: |
      Cellranger aggregation CSV file. If provided, the Identity metadata
      column will be added to the meta.csv


outputs:

  html_data:
    type: Directory
    outputBinding:
      glob: "cellbrowser_output/html_data"

  index_html_file:
    type: File
    outputBinding:
      glob: "cellbrowser_output/html_data/index.html"

  stdout_log:
    type: stdout

  stderr_log:
    type: stderr


baseCommand: ["bash", "-c"]


stdout: cbbuild_stdout.log
stderr: cbbuild_stderr.log


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

$schemas:
- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf

label: "Cell Ranger Count/Aggregate to UCSC Cell Browser"
s:name: "Cell Ranger Count/Aggregate to UCSC Cell Browser"
s:alternateName: |
  Exports clustering results from Cell Ranger Count Gene Expression or Cell Ranger
  Aggregate experiments into compatible with UCSC Cell Browser format

s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/sc-seq-analysis/main/tools/cellbrowser-build-cellranger.cwl
s:codeRepository: https://github.com/Barski-lab/sc-seq-analysis
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


doc: |
  Cell Ranger Count/Aggregate to UCSC Cell Browser

  Exports clustering results from Cell Ranger Count Gene Expression
  and Cell Ranger Aggregate experiments into compatible with UCSC
  Cell Browser format.