fasta_index_bismark_bwameth

Generate index files from reference fasta for bismark and bwameth

bismarkbwamethprepare genomeindex

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fasta_index_bismark_bwameth

Description

Generate index files from reference fasta for bismark and bwameth

Input

name

description

pattern

`fasta`

Reference genome
Structure: [ val(meta), path(fasta) ]

*.{fa/fa.gz}

`fasta_index`

Reference genome index file
Structure: [ val(meta), path(fasta) ]

*.fai

`bismark_index`

Bismark genome index files
Structure: [ val(meta), path(bismark_index) ]

`bwameth_index`

Bwameth genome index files
Structure: [ val(meta), path(bwameth_index) ]

`aligner`

Aligner name (bismark, bismark_hisat, or bwameth)

`collecthsmetrics`

Whether to run picard collecthsmetrics tool

Output

name

description

pattern

`fasta`

Reference genome
Structure: [ val(meta), path(fasta) ]

*.fa

`fasta_index`

Reference genome index file
Structure: [ val(meta), path(fasta) ]

*.fai

`bismark_index`

Bismark genome index files
Structure: [ val(meta), path(bismark_index) ]
pattern: “BismarkIndex”

`bwameth_index`

Bwameth genome index files
Structure: [ val(meta), path(bwameth_index) ]
pattern: “index”

`versions`

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml

fasta_index_bismark_bwameth

Description

Input

`fasta`

`fasta_index`

`bismark_index`

`bwameth_index`

`aligner`

`collecthsmetrics`

Output

`fasta`

`fasta_index`

`bismark_index`

`bwameth_index`

`versions`

included in

included modules and subworkflows

maintainers

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