modules/umitools_dedup

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

umitoolsdeduplicationdedup

https://github.com/nf-core/modules/[...]/modules/nf-core/umitools/dedup

Description

Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.

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}

`get_output_stats:boolean`

Whether or not to generate output stats.

Output

name:type

description

pattern

`bam`

`meta:map`

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

]

`${prefix}.bam:file`

BAM file with deduplicated UMIs.

*.{bam}

`log`

`meta:map`

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

]

`*.log:file`

File with logging information

*.{log}

`tsv_edit_distance`

`meta:map`

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

]

`*edit_distance.tsv:file`

Reports the (binned) average edit distance between the UMIs at each position.

*edit_distance.tsv

`tsv_per_umi`

`meta:map`

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

]

`*per_umi.tsv:file`

UMI-level summary statistics.

*per_umi.tsv

`tsv_umi_per_position`

`meta:map`

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

]

`*per_position.tsv:file`

Tabulates the counts for unique combinations of UMI and position.

*per_position.tsv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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

modules/umitools_dedup

Description

Input

`meta:map`

`bam:file`

`bai:file`

`get_output_stats:boolean`

Output

`bam`

`meta:map`

`${prefix}.bam:file`

`log`

`meta:map`

`*.log:file`

`tsv_edit_distance`

`meta:map`

`*edit_distance.tsv:file`

`tsv_per_umi`

`meta:map`

`*per_umi.tsv:file`

`tsv_umi_per_position`

`meta:map`

`*per_position.tsv:file`

`versions`

`versions.yml:file`

Tools

umi_tools

included in

maintainers

get in touch