cellbrowser-build-cellranger-arc.cwl

cwlVersion: v1.0
class: CommandLineTool


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


requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entryname: cellbrowser_gex.conf
    entry: |
      name = "GEX"
      shortLabel="GEX"
      priority = 1
      geneIdType="auto"
      geneLabel="Gene"
      exprMatrix="exprMatrix.tsv.gz"
      meta="meta.csv"
      coords=[
          {
              "file": "tsne.coords.csv",
              "shortLabel": "t-SNE"
          },
          {
              "file": "umap.coords.csv",
              "shortLabel": "UMAP"
          }
      ]
      markers=[
      {
          "file":"markers.tsv",
          "shortLabel":"Cluster-specific genes"
      }
      ]
      enumFields = ["Barcode"]
      clusterField="Cluster"
      labelField="Cluster"
      dataRoot="../"
  - entryname: cellbrowser_atac.conf
    entry: |
      name = "ATAC"
      shortLabel="ATAC"
      priority = 1
      geneIdType="auto"
      geneLabel="Peak"
      exprMatrix="exprMatrix.tsv.gz"
      meta="meta.csv"
      coords=[
          {
              "file": "tsne.coords.csv",
              "shortLabel": "t-SNE"
          },
          {
              "file": "umap.coords.csv",
              "shortLabel": "UMAP"
          },
          {
              "file": "lsa.coords.csv",
              "shortLabel": "LSA"
          }
      ]
      markers=[
      {
          "file":"markers.tsv",
          "shortLabel":"Cluster-specific peaks"
      }
      ]
      enumFields = ["Barcode"]
      clusterField="Cluster"
      labelField="Cluster"
      dataRoot="../"
  - entryname: cellbrowser.conf
    entry: |
      shortLabel="Multiome"
  - entryname: desc_gex.conf
    entry: |
      title = "GEX"
      abstract = ""
      methods = ""
      biorxiv_url = ""
      custom = {}
  - entryname: desc_atac.conf
    entry: |
      title = "ATAC"
      abstract = ""
      methods = ""
      biorxiv_url = ""
      custom = {}

inputs:

  bash_script:
    type: string?
    default: |
      #!/bin/bash
      echo "Preparing ATAC data"
      mkdir -p ./atac_input/analysis/clustering/graphclust \
              ./atac_input/analysis/diffexp/graphclust \
              ./atac_input/analysis/tsne/2_components \
              ./atac_input/analysis/umap/2_components \
              ./atac_input/analysis/lsa/2_components
      cp -r $0/clustering/atac/graphclust/clusters.csv ./atac_input/analysis/clustering/graphclust/clusters.csv
      cp -r $0/clustering/atac/graphclust/differential_accessibility.csv ./atac_input/analysis/diffexp/graphclust/differential_expression.csv
      cp -r $0/dimensionality_reduction/atac/tsne_projection.csv ./atac_input/analysis/tsne/2_components/projection.csv
      cp -r $0/dimensionality_reduction/atac/umap_projection.csv ./atac_input/analysis/umap/2_components/projection.csv
      cp -r $0/dimensionality_reduction/atac/lsa_projection.csv ./atac_input/analysis/lsa/2_components/projection.csv
      mkdir -p ./atac_input/filtered_feature_bc_matrix
      cp -r $1/* ./atac_input/filtered_feature_bc_matrix/
      echo "Importing ATAC data"
      cbImportCellranger -i atac_input -o atac --name atac
      cd ./atac
      echo "Copying coordinates files"
      cp ../atac_input/analysis/tsne/2_components/projection.csv tsne.coords.csv
      cp ../atac_input/analysis/umap/2_components/projection.csv umap.coords.csv
      cp ../atac_input/analysis/lsa/2_components/projection.csv lsa.coords.csv
      echo "Replacing configuration files"
      rm -f cellbrowser.conf desc.conf
      cp ../cellbrowser_atac.conf cellbrowser.conf
      cp ../desc_atac.conf 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
      cd ..
      echo "Preparing GEX data"
      mkdir -p ./gex_input/analysis/clustering/graphclust \
              ./gex_input/analysis/diffexp/graphclust \
              ./gex_input/analysis/tsne/2_components \
              ./gex_input/analysis/umap/2_components
      cp -r $0/clustering/gex/graphclust/clusters.csv ./gex_input/analysis/clustering/graphclust/clusters.csv
      cp -r $0/clustering/gex/graphclust/differential_expression.csv ./gex_input/analysis/diffexp/graphclust/differential_expression.csv
      cp -r $0/dimensionality_reduction/gex/tsne_projection.csv ./gex_input/analysis/tsne/2_components/projection.csv
      cp -r $0/dimensionality_reduction/gex/umap_projection.csv ./gex_input/analysis/umap/2_components/projection.csv
      mkdir -p ./gex_input/filtered_feature_bc_matrix
      cp -r $1/* ./gex_input/filtered_feature_bc_matrix/
      echo "Importing GEX data"
      cbImportCellranger -i gex_input -o gex --name gex
      cd ./gex
      echo "Copying coordinates files"
      cp ../gex_input/analysis/tsne/2_components/projection.csv tsne.coords.csv
      cp ../gex_input/analysis/umap/2_components/projection.csv umap.coords.csv
      echo "Replacing configuration files"
      rm -f cellbrowser.conf desc.conf
      cp ../cellbrowser_gex.conf cellbrowser.conf
      cp ../desc_gex.conf 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
      cd ..
      echo "Building"
      cbBuild -r -o html_data
      echo "Cleaning up temporary files"
      rm -rf gex_input atac_input atac gex
    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 ARC
      Count or Cellranger ARC 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 ARC Count or Cellranger ARC 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: "html_data"

  index_html_file:
    type: File
    outputBinding:
      glob: "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 ARC Count/Aggregate to UCSC Cell Browser"
s:name: "Cell Ranger ARC Count/Aggregate to UCSC Cell Browser"
s:alternateName: |
  Exports clustering results from Cell Ranger ARC Count Chromatin Accessibility and Gene Expression or
  Cell Ranger ARC 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-arc.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 ARC Count/Aggregate to UCSC Cell Browser

  Exports clustering results from Cell Ranger ARC Count
  Chromatin Accessibility and Gene Expression or Cell
  Ranger ARC Aggregate experiments into compatible with
  UCSC Cell Browser format