modules/biscuit_epiread

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

biscuitDNA methylationWGBSscWGBSbisulfite sequencingalignerbam

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

Description

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file contained mapped reads

`meta2`
`:map`

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

`bai`
`:file`

BAM file index

`meta3`
`:map`

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

`snp_bed`
`:file`

BED file containing SNP information (optional)

`meta4`
`:map`

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

`fasta`
`:file`

Input genome fasta file

`meta5`
`: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

`bed`

`meta`
`:map`

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

`*.bed.gz`
`:file`

Gzipped BED file with methylation (and optionally SNV) information

*.{epiread.bed.gz}

`versions_biscuit`

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

The name of the process

`biscuit`
`:string`

The name of the tool

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

The expression to obtain the version of the tool

`versions_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`biscuit`
`:string`

The name of the tool

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

Tools

biscuit
MIT

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

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/epiread_format https://github.com/huishenlab/biscuit

modules/biscuit_epiread

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`snp_bed`
`:file`

`meta4`
`:map`

`fasta`
`:file`

`meta5`
`:map`

`index`
`:directory`

Output

`bed`

`meta`
`:map`

`*.bed.gz`
`:file`

`versions_biscuit`

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

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

Topics

`versions`

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

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

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

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

Tools

biscuit
MIT

maintainers

get in touch

modules/biscuit_epiread

Description

Input

meta:map

bam:file

meta2:map

bai:file

meta3:map

snp_bed:file

meta4:map

fasta:file

meta5:map

index:directory

Output

bed

meta:map

*.bed.gz:file

versions_biscuit

${task.process}:string

biscuit:string

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //':eval

versions_samtools

${task.process}:string

samtools:string

samtools --version |& sed '1!d; s/^.*samtools //':eval

Topics

versions

${task.process}:string

biscuit:string

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //':eval

${task.process}:string

samtools:string

samtools --version |& sed '1!d; s/^.*samtools //':eval

Tools

biscuit MIT

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`snp_bed`
`:file`

`meta4`
`:map`

`fasta`
`:file`

`meta5`
`:map`

`index`
`:directory`

`bed`

`meta`
`:map`

`*.bed.gz`
`:file`

`versions_biscuit`

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

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

`versions_samtools`

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

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

`versions`

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

`biscuit`
`:string`

`biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'`
`:eval`

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

`samtools`
`:string`

`samtools --version |& sed '1!d; s/^.*samtools //'`
`:eval`

biscuit
MIT