modules/tidk_explore

tidk explore attempts to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT).

genomicstelomeresearch

https://github.com/nf-core/modules/[...]/modules/nf-core/tidk/explore

Description

tidk explore attempts to find the simple telomeric repeat unit in the genome provided. It will report this repeat in its canonical form (e.g. TTAGG -> AACCT).

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

The input fasta file

*.{fsa,fa,fasta}

Output

name:type

description

pattern

`explore_tsv`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.tidk.explore.tsv`
`:file`

Telomeres and their frequencies in TSV format

*.tidk.explore.tsv

`top_sequence`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.top.sequence.txt`
`:file`

The most frequent telomere sequence if one or more sequences are identified by the toolkit

*.top.sequence.txt

`versions_tidk`

`${task.process}`
`:string`

The name of the process

`tidk`
`:string`

The name of the tool

`tidk --version | sed 's/tidk //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`tidk`
`:string`

The name of the tool

`tidk --version | sed 's/tidk //'`
`:eval`

The expression to obtain the version of the tool

Tools

tidk
MIT

tidk is a toolkit to identify and visualise telomeric repeats in genomes

github.com/tolkit/telomeric-identifier 10.5281/zenodo.10091385

modules/tidk_explore

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`explore_tsv`

`meta`
`:map`

`*.tidk.explore.tsv`
`:file`

`top_sequence`

`meta`
`:map`

`*.top.sequence.txt`
`:file`

`versions_tidk`

`${task.process}`
`:string`

`tidk`
`:string`

`tidk --version | sed 's/tidk //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`tidk`
`:string`

`tidk --version | sed 's/tidk //'`
`:eval`

Tools

tidk
MIT

included in

maintainer

get in touch

modules/tidk_explore

Description

Input

meta:map

fasta:file

Output

explore_tsv

meta:map

*.tidk.explore.tsv:file

top_sequence

meta:map

*.top.sequence.txt:file

versions_tidk

${task.process}:string

tidk:string

tidk --version | sed 's/tidk //':eval

Topics

versions

${task.process}:string

tidk:string

tidk --version | sed 's/tidk //':eval

Tools

tidk MIT

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`explore_tsv`

`meta`
`:map`

`*.tidk.explore.tsv`
`:file`

`top_sequence`

`meta`
`:map`

`*.top.sequence.txt`
`:file`

`versions_tidk`

`${task.process}`
`:string`

`tidk`
`:string`

`tidk --version | sed 's/tidk //'`
`:eval`

`versions`

`${task.process}`
`:string`

`tidk`
`:string`

`tidk --version | sed 's/tidk //'`
`:eval`

tidk
MIT