subworkflows_single_cell_rnaseq.cwl

Documentation for single_cell_rnaseq.cwl

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Overview

Running cellranger count and lineage inference

Inputs

Name	Label	Description	Type	Secondary Files
chemistry			string?
reference			Directory
sample_name			string
fastq_directory			Directory[]
lineage_min_cells			int?
lineage_min_features			int?
lineage_reference_data			string

Outputs

Name	Label	Description	Type	Secondary Files
counts_out_dir			Directory
lineage_cellmatch_lineage_out_dir			Directory

Steps

Name	CWL Run
count	tools/cellranger_count.cwl
lineage	tools/cellmatch_lineage.cwl