Workflow: wf_demultiplex_se.cwl

Fetched 2020-07-14 15:08:19 GMT

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)

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Inputs

ID Type Title Doc
read
dataset String

Steps

ID Runs Label Doc
gzip_demux
gzip.cwl (CommandLineTool)
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]

Outputs

ID Type Label Doc
A_output_demuxed_read1 File
read_name String
dataset_name String
Permalink: https://w3id.org/cwl/view/git/6b533898c395e9e5b9d0acc1587d0c68bc56abe0/cwl/wf_demultiplex_se.cwl