modules/biscuit_mergecg

Merges methylation information for opposite-strand C’s in a CpG context

biscuitDNA methylationWGBSscWGBSbisulfite sequencingalignerbed

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

Description

Merges methylation information for opposite-strand C’s in a CpG context

Input

name:type

description

pattern

`meta`
`:map`

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

`bed`
`:file`

Biscuit BED file (output of biscuit vcf2bed)

`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

`bed`

`meta`
`:map`

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

`*.bed.gz`
`:file`

Gzipped BED file with merged methylation information

*.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/docs/methylextraction https://github.com/huishenlab/biscuit

modules/biscuit_mergecg

Description

Input

`meta`
`:map`

`bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`: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_mergecg

Description

Input

meta :map

bed :file

meta2 :map

fasta :file

meta3 :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

biscuitMIT

maintainers

get in touch

`meta`
`:map`

`bed`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`: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