modules/bismark_genomepreparation

Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.

bismark3-letter genomeindexmethylation5mCmethylseqbisulphitebisulfitefasta

https://github.com/nf-core/modules/[...]/modules/nf-core/bismark/genomepreparation

Description

Converts a specified reference genome into two different bisulfite converted versions and indexes them for alignments.

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`fasta{:bash}`
`:file`

Input genome fasta file

Output

name:type

description

pattern

`index{:bash}`

`meta{:bash}`
`:map`

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

`BismarkIndex{:bash}`
`:directory`

Bismark genome index directory

BismarkIndex

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

bismark
GPL-3.0-or-later

Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.

github.com/FelixKrueger/Bismark github.com/FelixKrueger/Bismark[...]Docs 10.1093/bioinformatics/btr167

modules/bismark_genomepreparation

Description

Input

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

Output

`index{:bash}`

`meta{:bash}`
`:map`

`BismarkIndex{:bash}`
`:directory`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

bismark
GPL-3.0-or-later

included in

maintainers

get in touch

modules/bismark_genomepreparation

Description

Input

meta{:bash}:map

fasta{:bash}:file

Output

index{:bash}

meta{:bash}:map

BismarkIndex{:bash}:directory

versions{:bash}

versions.yml{:bash}:file

Tools

bismark GPL-3.0-or-later

included in

maintainers

get in touch

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

`index{:bash}`

`meta{:bash}`
`:map`

`BismarkIndex{:bash}`
`:directory`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

bismark
GPL-3.0-or-later