CWL Workflow: wf_demultiplex_se.cwl

Workflow: wf_demultiplex_se.cwl

Fetched 2023-01-14 15:19:29 GMT

Verified with cwltool version 3.1.20221201130942

This workflow takes in single-end reads, and performs the following steps in order: demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)

Selected
|
Default Values
Nested Workflows
Tools
Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: BSD 3-clause "New" or "Revised" License

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

Inputs

ID	Type	Title	Doc
read
dataset	String

Steps

ID	Runs	Label	Doc
AB_demux	demux_se.cwl (CommandLineTool)		Extract UMI barcode from a read and add it to the read name, leaving any sample barcode in place. Can deal with paired end reads and UMIs split across the paired ends. For eCLIP single-end processing, this step just trims the first 10 bases, but named as such to match the demux_pe step. Usage: umi_tools extract --bc-pattern=[PATTERN] -L extract.log [OPTIONS]
gzip_demux	gzip.cwl (CommandLineTool)

Outputs

ID	Type	Label	Doc
read_name	String
dataset_name	String
A_output_demuxed_read1	File

html json turtle jsonld rdfxml svg png dot zip ro yaml raw

Permalink: https://w3id.org/cwl/view/git/6b533898c395e9e5b9d0acc1587d0c68bc56abe0/cwl/wf_demultiplex_se.cwl