Description

Group reads based on their UMI and mapping coordinates

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM file containing reads to be deduplicated via UMIs.

*.{bam}

bai (file)

BAM index files corresponding to the input BAM file.

*.{bai}

create_bam (boolean)

Whether or not to create a read group tagged BAM file.

get_group_info (boolean)

Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

a read group tagged BAM file.

${prefix}.{bam}

log (file)

File with logging information

*.{log}

tsv (file)

Flatfile describing the read groups, see docs for complete info of all columns

*.{tsv}
author
Github user Joon-Klaps
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Tools

umi_tools

UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

umi-tools.readthedocs.io/en/latest