CWL Workflow: wf_cellranger.cwl

This workflow is Open Source and may be reused according to the terms of: GNU Affero General Public License v3.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
pi_name	String
samples	14a758dd63e5010dbe6e65c0cb2e5c24[]
organism	String
investigator	String
aggr_nickname	String
contact_email	String
transcriptome	Directory
assay_protocol	String
processing_date	String
sequencing_date	String
aggr_norm_method	String
library_strategy	String
sequencing_center	String
experiment_summary	String
experiment_nickname	String
experiment_start_date	String
growth_protocol_description	String
extract_protocol_description	String
library_construction_protocol	String
treatment_protocol_description	String

ID	Runs	Doc
step_parse_samples	parse_samples.cwl (ExpressionTool)	This tool parses an array of records, with each record containing Usage:
step_cellranger_aggr	cellranger_aggr.cwl (CommandLineTool)	The javascript entry creates the aggregate.csv manifest. The commandlinetool calls cellranger aggregate based on the aggregate.csv, which was created from the list of h5_basedirs specified.
step_cellranger_count	cellranger_count.cwl (CommandLineTool)

ID	Type	Label	Doc
output_aggr_dir	Directory
output_single_dir	Directory[]