modules/biscuit_align

Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.

biscuitDNA methylationWGBSscWGBSbisulfite sequencingalignerbam

https://github.com/nf-core/modules/[...]/modules/nf-core/biscuit/align

Description

Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit.

Input

name:type

description

pattern

`meta:map`

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

`reads:file`

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

`meta2:map`

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

`fasta:file`

Input genome fasta file

`meta3:map`

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

`index:directory`

Directory containing biscuit genome index

Output

name:type

description

pattern

`bam`

`meta:map`

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

`*.bam:file`

Output BAM file containing read alignments

*.{bam}

`bai`

`meta:map`

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

`*.bai:file`

Output BAM index

*.{bai}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/docs/alignment https://github.com/huishenlab/biscuit

modules/biscuit_align

Description

Input

meta:map

reads:file

meta2:map

fasta:file

meta3:map

index:directory

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

versions

versions.yml:file

Tools

biscuit MIT

`meta:map`

`reads:file`

`meta2:map`

`fasta:file`

`meta3:map`

`index:directory`

`bam`

`meta:map`

`*.bam:file`

`bai`

`meta:map`

`*.bai:file`

`versions`

`versions.yml:file`

biscuit
MIT