tools_cellranger_feature_barcoding.cwl

Documentation for cellranger_feature_barcoding.cwl

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Overview

Run Cell Ranger Count with feature barcoding

Docker Requirement

registry.gsc.wustl.edu/alex.paul/cellranger:6.0.0

Inputs

Name	Label	Description	Type	Secondary Files
antibody_fastq_directory		Array of directories containing fastq files with antibody feature barcoding	Directory[]
antibody_sample_names		Sample name, must be same as name specified in sample sheet in previous mkfastq step	string[]
chemistry		Assay configuration used, default 'auto' should usually work without issue	string?
expression_fastq_directory		Array of directories containing fastq files for gene expression	Directory[]
expression_sample_names		Sample name, must be same as name specified in sample sheet in previous mkfastq step	string[]
feature_reference_csv		Feature reference csv for the antibody barcodes	File
reference		Transcriptome reference compatible with input species and Cell Ranger	Directory
run_name		Used to generate the run id	string

Outputs

Name	Label	Description	Type	Secondary Files
libraries_csv			File
out_dir			Directory