sc-ctype-assign.cwl

cwlVersion: v1.0
class: CommandLineTool


requirements:
- class: InlineJavascriptRequirement
- class: EnvVarRequirement
  envDef:
    R_MAX_VSIZE: $((inputs.vector_memory_limit * 1000000000).toString())


hints:
- class: DockerRequirement
  dockerPull: biowardrobe2/sc-tools:v0.0.13


inputs:

  query_data_rds:
    type: File
    inputBinding:
      prefix: "--query"
    doc: |
      Path to the RDS file to load Seurat object from. This file should include
      genes expression and/or chromatin accessibility information stored in the RNA
      and ATAC assays correspondingly. Additionally, 'rnaumap', and/or 'atacumap',
      and/or 'wnnumap' dimensionality reductions should be present.

  cell_type_data:
    type: File
    inputBinding:
      prefix: "--celltypes"
    doc: |
      Path to the TSV/CSV file for manual cell type assignment for each of the clusters.
      First column - 'cluster', second column may have arbitrary name.

  query_source_column:
    type: string
    inputBinding:
      prefix: "--source"
    doc: |
      Column from the metadata of the loaded Seurat object to select clusters from.

  query_target_column:
    type: string
    inputBinding:
      prefix: "--target"
    doc: |
      Column from the metadata of the loaded Seurat object to save manually
      assigned cell types.

  atac_fragments_file:
    type: File?
    secondaryFiles:
    - .tbi
    inputBinding:
      prefix: "--fragments"
    doc: |
      Count and barcode information for every ATAC fragment used in the loaded Seurat
      object. File should be saved in TSV format with tbi-index file. Ignored if the
      loaded Seurat object doesn't include ATAC assay.

  genes_of_interest:
    type:
    - "null"
    - string
    - string[]
    inputBinding:
      prefix: "--genes"
    doc: |
      Genes of interest to build gene expression and/or Tn5 insertion frequency plots
      for the nearest peaks. To build gene expression plots the loaded Seurat object
      should include RNA assay. To build Tn5 insertion frequency plots for the nearest
      peaks the loaded Seurat object should include ATAC assay as well as the --fragments
      file should be provided.
      Default: None

  export_pdf_plots:
    type: boolean?
    inputBinding:
      prefix: "--pdf"
    doc: |
      Export plots in PDF.
      Default: false

  color_theme:
    type:
    - "null"
    - type: enum
      symbols:
      - "gray"
      - "bw"
      - "linedraw"
      - "light"
      - "dark"
      - "minimal"
      - "classic"
      - "void"
    inputBinding:
      prefix: "--theme"
    doc: |
      Color theme for all generated plots. One of gray, bw, linedraw, light,
      dark, minimal, classic, void.
      Default: classic

  verbose:
    type: boolean?
    inputBinding:
      prefix: "--verbose"
    doc: |
      Print debug information.
      Default: false

  export_h5seurat_data:
    type: boolean?
    inputBinding:
      prefix: "--h5seurat"
    doc: |
      Save Seurat data to h5seurat file.
      Default: false

  export_h5ad_data:
    type: boolean?
    inputBinding:
      prefix: "--h5ad"
    doc: |
      Save Seurat data to h5ad file.
      Default: false

  export_ucsc_cb:
    type: boolean?
    inputBinding:
      prefix: "--cbbuild"
    doc: |
      Export results to UCSC Cell Browser. Default: false

  output_prefix:
    type: string?
    inputBinding:
      prefix: "--output"
    doc: |
      Output prefix.
      Default: ./sc

  parallel_memory_limit:
    type: int?
    inputBinding:
      prefix: "--memory"
    doc: |
      Maximum memory in GB allowed to be shared between the workers
      when using multiple --cpus.
      Default: 32

  vector_memory_limit:
    type: int?
    default: 128
    doc: |
      Maximum vector memory in GB allowed to be used by R.
      Default: 128

  threads:
    type: int?
    inputBinding:
      prefix: "--cpus"
    doc: |
      Number of cores/cpus to use.
      Default: 1


outputs:

  umap_rd_rnaumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_rd_rnaumap.png"
    doc: |
      Cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  umap_rd_rnaumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_rd_rnaumap.pdf"
    doc: |
      Cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  umap_rd_atacumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_rd_atacumap.png"
    doc: |
      Cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  umap_rd_atacumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_rd_atacumap.pdf"
    doc: |
      Cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  umap_rd_wnnumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_rd_wnnumap.png"
    doc: |
      Cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  umap_rd_wnnumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_rd_wnnumap.pdf"
    doc: |
      Cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  umap_spl_idnt_rd_rnaumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_rnaumap.png"
    doc: |
      Split by dataset cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  umap_spl_idnt_rd_rnaumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_rnaumap.pdf"
    doc: |
      Split by dataset cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  umap_spl_idnt_rd_atacumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_atacumap.png"
    doc: |
      Split by dataset cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  umap_spl_idnt_rd_atacumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_atacumap.pdf"
    doc: |
      Split by dataset cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  umap_spl_idnt_rd_wnnumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_wnnumap.png"
    doc: |
      Split by dataset cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  umap_spl_idnt_rd_wnnumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_idnt_rd_wnnumap.pdf"
    doc: |
      Split by dataset cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  umap_spl_cnd_rd_rnaumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_rnaumap.png"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  umap_spl_cnd_rd_rnaumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_rnaumap.pdf"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  umap_spl_cnd_rd_atacumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_atacumap.png"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  umap_spl_cnd_rd_atacumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_atacumap.pdf"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  umap_spl_cnd_rd_wnnumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_wnnumap.png"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  umap_spl_cnd_rd_wnnumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_cnd_rd_wnnumap.pdf"
    doc: |
      Split by grouping condition cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  umap_spl_ph_rd_rnaumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_rnaumap.png"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  umap_spl_ph_rd_rnaumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_rnaumap.pdf"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  umap_spl_ph_rd_atacumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_atacumap.png"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  umap_spl_ph_rd_atacumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_atacumap.pdf"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  umap_spl_ph_rd_wnnumap_plot_png:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_wnnumap.png"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  umap_spl_ph_rd_wnnumap_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_umap_spl_ph_rd_wnnumap.pdf"
    doc: |
      Split by cell cycle phase cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  cmp_gr_ctyp_spl_idnt_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ctyp_spl_idnt.png"
    doc: |
      Grouped by cell type split by dataset cells composition plot. Downsampled.
      PNG format

  cmp_gr_ctyp_spl_idnt_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ctyp_spl_idnt.pdf"
    doc: |
      Grouped by cell type split by dataset cells composition plot. Downsampled.
      PDF format

  cmp_gr_idnt_spl_ctyp_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_idnt_spl_ctyp.png"
    doc: |
      Grouped by dataset split by cell type cells composition plot. Downsampled.
      PNG format

  cmp_gr_idnt_spl_ctyp_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_idnt_spl_ctyp.pdf"
    doc: |
      Grouped by dataset split by cell type cells composition plot. Downsampled.
      PDF format

  cmp_gr_ph_spl_idnt_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ph_spl_idnt.png"
    doc: |
      Grouped by cell cycle phase split by dataset cells composition plot. Downsampled.
      PNG format

  cmp_gr_ph_spl_idnt_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ph_spl_idnt.pdf"
    doc: |
      Grouped by cell cycle phase split by dataset cells composition plot. Downsampled.
      PDF format

  cmp_gr_ctyp_spl_cnd_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ctyp_spl_cnd.png"
    doc: |
      Grouped by cell type split by condition cells composition plot. Downsampled.
      PNG format

  cmp_gr_ctyp_spl_cnd_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ctyp_spl_cnd.pdf"
    doc: |
      Grouped by cell type split by condition cells composition plot. Downsampled.
      PDF format

  cmp_gr_cnd_spl_ctyp_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_cnd_spl_ctyp.png"
    doc: |
      Grouped by condition split by cell type cells composition plot. Downsampled.
      PNG format

  cmp_gr_cnd_spl_ctyp_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_cnd_spl_ctyp.pdf"
    doc: |
      Grouped by condition split by cell type cells composition plot. Downsampled.
      PDF format

  cmp_gr_ph_spl_ctyp_plot_png:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ph_spl_ctyp.png"
    doc: |
      Grouped by cell cycle phase split by cell type cells composition plot. Downsampled.
      PNG format

  cmp_gr_ph_spl_ctyp_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_cmp_gr_ph_spl_ctyp.pdf"
    doc: |
      Grouped by cell cycle phase split by cell type cells composition plot. Downsampled.
      PDF format

  xpr_avg_plot_png:
    type: File?
    outputBinding:
      glob: "*_xpr_avg.png"
    doc: |
      Log normalized scaled average gene expression per cell type.
      PNG format

  xpr_avg_plot_pdf:
    type: File?
    outputBinding:
      glob: "*_xpr_avg.pdf"
    doc: |
      Log normalized scaled average gene expression per cell type.
      PDF format

  xpr_dnst_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_dnst_*.png"
    doc: |
      Log normalized gene expression density per cell type.
      PNG format

  xpr_dnst_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_dnst_*.pdf"
    doc: |
      Log normalized gene expression density per cell type.
      PDF format

  xpr_per_cell_rd_rnaumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_rnaumap_*.png"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  xpr_per_cell_rd_rnaumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_rnaumap_*.pdf"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  xpr_per_cell_rd_atacumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_atacumap_*.png"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  xpr_per_cell_rd_atacumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_atacumap_*.pdf"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  xpr_per_cell_rd_wnnumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_wnnumap_*.png"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  xpr_per_cell_rd_wnnumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_rd_wnnumap_*.pdf"
    doc: |
      Log normalized gene expression on cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  xpr_per_cell_sgnl_rd_rnaumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_rnaumap_*.png"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (rnaumap dim. reduction).
      PNG format

  xpr_per_cell_sgnl_rd_rnaumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_rnaumap_*.pdf"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (rnaumap dim. reduction).
      PDF format

  xpr_per_cell_sgnl_rd_atacumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_atacumap_*.png"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (atacumap dim. reduction).
      PNG format

  xpr_per_cell_sgnl_rd_atacumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_atacumap_*.pdf"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (atacumap dim. reduction).
      PDF format

  xpr_per_cell_sgnl_rd_wnnumap_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_wnnumap_*.png"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (wnnumap dim. reduction).
      PNG format

  xpr_per_cell_sgnl_rd_wnnumap_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_xpr_per_cell_sgnl_rd_wnnumap_*.pdf"
    doc: |
      Log normalized gene expression density on cells UMAP with assigned cell types (wnnumap dim. reduction).
      PDF format

  cvrg_plot_png:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_cvrg_*.png"
    doc: |
      Tn5 insertion frequency plot around gene.
      PNG format

  cvrg_plot_pdf:
    type:
    - "null"
    - type: array
      items: File
    outputBinding:
      glob: "*_cvrg_*.pdf"
    doc: |
      Tn5 insertion frequency plot around gene.
      PDF format

  ucsc_cb_config_data:
    type: Directory?
    outputBinding:
      glob: "*_cellbrowser"
    doc: |
      Directory with UCSC Cellbrowser configuration data.

  ucsc_cb_html_data:
    type: Directory?
    outputBinding:
      glob: "*_cellbrowser/html_data"
    doc: |
      Directory with UCSC Cellbrowser html data.

  ucsc_cb_html_file:
    type: File?
    outputBinding:
      glob: "*_cellbrowser/html_data/index.html"
    doc: |
      HTML index file from the directory with UCSC Cellbrowser html data.

  seurat_data_rds:
    type: File
    outputBinding:
      glob: "*_data.rds"
    doc: |
      Reduced Seurat data in RDS format

  seurat_data_h5seurat:
    type: File?
    outputBinding:
      glob: "*_data.h5seurat"
    doc: |
      Reduced Seurat data in h5seurat format

  seurat_data_h5ad:
    type: File?
    outputBinding:
      glob: "*_data.h5ad"
    doc: |
      Reduced Seurat data in h5ad format

  stdout_log:
    type: stdout

  stderr_log:
    type: stderr


baseCommand: ["sc_ctype_assign.R"]

stdout: sc_ctype_assign_stdout.log
stderr: sc_ctype_assign_stderr.log


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

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


label: "Single-cell Manual Cell Type Assignment"
s:name: "Single-cell Manual Cell Type Assignment"
s:alternateName: "Assigns cell types for clusters based on the provided metadata file"

s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/sc-ctype-assign.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


doc: |
  Single-cell Manual Cell Type Assignment

  Assigns cell types for clusters based on the provided metadata file.


s:about: |
  usage: sc_ctype_assign.R [-h] --query QUERY --celltypes
                                          CELLTYPES --source SOURCE --target
                                          TARGET [--fragments FRAGMENTS]
                                          [--genes [GENES [GENES ...]]] [--pdf]
                                          [--verbose] [--h5seurat] [--h5ad]
                                          [--cbbuild] [--output OUTPUT]
                                          [--theme {gray,bw,linedraw,light,dark,minimal,classic,void}]
                                          [--cpus CPUS] [--memory MEMORY]

  Single-cell Manual Cell Type Assignment

  optional arguments:
    -h, --help            show this help message and exit
    --query QUERY         Path to the RDS file to load Seurat object from. This
                          file should include genes expression and/or chromatin
                          accessibility information stored in the RNA and ATAC
                          assays correspondingly. Additionally, 'rnaumap',
                          and/or 'atacumap', and/or 'wnnumap' dimensionality
                          reductions should be present.
    --celltypes CELLTYPES
                          Path to the TSV/CSV file for manual cell type
                          assignment for each of the clusters. First column -
                          'cluster', second column may have arbitrary name.
    --source SOURCE       Column from the metadata of the loaded Seurat object
                          to select clusters from.
    --target TARGET       Column from the metadata of the loaded Seurat object
                          to save manually assigned cell types.
    --fragments FRAGMENTS
                          Count and barcode information for every ATAC fragment
                          used in the loaded Seurat object. File should be saved
                          in TSV format with tbi-index file. Ignored if the
                          loaded Seurat object doesn't include ATAC assay.
    --genes [GENES [GENES ...]]
                          Genes of interest to build gene expression and/or Tn5
                          insertion frequency plots for the nearest peaks. To
                          build gene expression plots the loaded Seurat object
                          should include RNA assay. To build Tn5 insertion
                          frequency plots for the nearest peaks the loaded
                          Seurat object should include ATAC assay as well as the
                          --fragments file should be provided. Default: None
    --pdf                 Export plots in PDF. Default: false
    --verbose             Print debug information. Default: false
    --h5seurat            Save Seurat data to h5seurat file. Default: false
    --h5ad                Save Seurat data to h5ad file. Default: false
    --cbbuild             Export results to UCSC Cell Browser. Default: false
    --output OUTPUT       Output prefix. Default: ./sc
    --theme {gray,bw,linedraw,light,dark,minimal,classic,void}
                          Color theme for all generated plots. Default: classic
    --cpus CPUS           Number of cores/cpus to use. Default: 1
    --memory MEMORY       Maximum memory in GB allowed to be shared between the
                          workers when using multiple --cpus. Default: 32