Workflow: CODEX analysis pipeline using Cytokit

Fetched 2022-01-20 13:37:11 GMT
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Inputs

ID Type Title Doc
gpus String GPUs to use, represented as a comma-separated list of integers.
data_dir Directory Directory containing CODEX data

Steps

ID Runs Label Doc
cytokit_processor
steps/cytokit_processor.cwl (CommandLineTool)
CODEX analysis via Cytokit
collect_dataset_info
steps/collect_dataset_info.cwl (CommandLineTool)
Collect dataset info for Cytokit
ome_tiff_creation
steps/ome_tiff_creation.cwl (CommandLineTool)
Create OME-TIFF versions of Cytokit segmentation and extract results
run_sprm
steps/run_sprm.cwl (CommandLineTool)
Run Spatial Process & Relationship Modeling (SPRM)
create_yaml_config
steps/create_yaml_config.cwl (CommandLineTool)
Create Cytokit experiment config
create_dir_for_viz
steps/create_dir_for_viz.cwl (CommandLineTool)
Create directory containing symlinks to relevant files for visualization team
cytokit_operator
steps/cytokit_operator.cwl (CommandLineTool)
CODEX analysis via Cytokit

Outputs

ID Type Label Doc
experiment_config File Cytokit configuration format
sprm_output_dir Directory Directory containing all SPRM outputs
ome_tiff_output Directory Segmentation masks in OME-TIFF format
for_viz_dir File Archive of symbolic links to files for visualization team
Permalink: https://w3id.org/cwl/view/git/a04e55b0fd73afbed8d29b2040dd9c438ba666a6/pipeline.cwl