/
soupx-subworkflow.cwl
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soupx-subworkflow.cwl
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cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: MultipleInputFeatureRequirement
inputs:
raw_feature_bc_matrices_folder:
type: File
doc: "Compressed folder with unfiltered feature-barcode matrices"
filtered_feature_bc_matrix_folder:
type: File
doc: "Compressed folder with filtered feature-barcode matrices"
secondary_analysis_report_folder:
type: File
doc: "Compressed folder with secondary analysis results"
genelist_file:
type: File?
doc: "Target genes list. Headerless text file with 1 gene per line"
expression_threshold:
type: float?
doc: "Expression threshold for displaying target genes on a plot (expression > threshold)"
fdr:
type: float?
doc: "FDR cutoff for expression ratio plots"
round_counts:
type: boolean?
doc: "Round adjusted counts to integers"
matrix_format_version:
type:
- "null"
- type: enum
name: "matrix_format_version"
symbols: ["2","3"]
doc: "Output matrix format version. Corresponds to the latest Cell Ranger matrix format"
output_prefix:
type: string?
doc: "Output prefix"
outputs:
adjusted_feature_bc_matrices_folder:
type: File
outputSource: compress_adjusted_feature_bc_matrices_folder/compressed_folder
doc: "Compressed folder with adjusted feature-barcode matrices in MEX format"
adjusted_feature_bc_matrices_h5:
type: File
outputSource: estimate_contamination/adjusted_feature_bc_matrices_h5
doc: "Adjusted feature-barcode matrices in HDF5 format"
contamination_estimation_plot:
type: File
outputSource: estimate_contamination/contamination_estimation_plot
doc: "Contamination estimation plot"
raw_gene_expression_plots:
type: File?
outputSource: estimate_contamination/raw_gene_expression_plots
doc: "Raw gene expression plots"
adjusted_gene_expression_plots:
type: File?
outputSource: estimate_contamination/adjusted_gene_expression_plots
doc: "Adjusted gene expression plots"
raw_gene_expression_to_pure_soup_ratio_plots:
type: File?
outputSource: estimate_contamination/raw_gene_expression_to_pure_soup_ratio_plots
doc: "Raw gene expression to pure soup ratio plots"
raw_to_adjusted_gene_expression_ratio_plots:
type: File?
outputSource: estimate_contamination/raw_to_adjusted_gene_expression_ratio_plots
doc: "Raw to adjusted gene expression ratio plots"
soupx_stdout_log:
type: File
outputSource: estimate_contamination/stdout_log
doc: "SoupX stdout log"
soupx_stderr_log:
type: File
outputSource: estimate_contamination/stderr_log
doc: "SoupX stderr log"
steps:
extract_count_matrices_to_folder:
run:
cwlVersion: v1.0
class: CommandLineTool
hints:
- class: DockerRequirement
dockerPull: scidap/scidap:v0.0.4
inputs:
script:
type: string?
default: |
set -- "$0" "$@"
mkdir counts && cd counts
for i in "$@";
do tar xvf $i;
done;
inputBinding:
position: 1
compressed_files:
type: File[]
inputBinding:
position: 2
outputs:
output_folder:
type: Directory
outputBinding:
glob: "counts"
baseCommand: [bash, '-c']
in:
compressed_files:
source:
- raw_feature_bc_matrices_folder
- filtered_feature_bc_matrix_folder
- secondary_analysis_report_folder
out:
- output_folder
estimate_contamination:
run: soupx.cwl
in:
feature_bc_matrices_folder: extract_count_matrices_to_folder/output_folder
genelist_file: genelist_file
expression_threshold: expression_threshold
fdr: fdr
round_counts: round_counts
matrix_format_version: matrix_format_version
output_prefix: output_prefix
out:
- adjusted_feature_bc_matrices_folder
- adjusted_feature_bc_matrices_h5
- contamination_estimation_plot
- raw_gene_expression_plots
- adjusted_gene_expression_plots
- raw_gene_expression_to_pure_soup_ratio_plots
- raw_to_adjusted_gene_expression_ratio_plots
- stdout_log
- stderr_log
compress_adjusted_feature_bc_matrices_folder:
run: tar-compress.cwl
in:
folder_to_compress: estimate_contamination/adjusted_feature_bc_matrices_folder
out:
- compressed_folder
$namespaces:
s: http://schema.org/
$schemas:
- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
s:name: "SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination"
label: "SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination"
s:alternateName: "SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination"
s:downloadUrl: https://raw.githubusercontent.com/Barski-lab/workflows/master/tools/soupx-subworkflow.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: |
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.
s:about: |
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.