modules/methyldackel_extract

Extracts per-base methylation metrics from alignments

methylation5mCmethylseqbisulphitebisulfiteconsensusbedGraphbamcram

https://github.com/nf-core/modules/[...]/modules/nf-core/methyldackel/extract

Description

Extracts per-base methylation metrics from alignments

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM file

*.{bam,cram}

`bai`
`:file`

BAM/CRAM index file

*.{bai,crai}

`meta2`
`:map`

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

`fasta`
`:file`

Input genome fasta file

*.{fasta,fa}

`fai`
`:file`

FASTA index file

*.{fai}

Output

name:type

description

pattern

`bedgraph`

`meta`
`:map`

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

`*.bedGraph`
`:file`

bedGraph file, containing per-base methylation metrics

*.bedGraph

`methylkit`

`meta`
`:map`

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

`*.methylKit`
`:file`

methylKit file, containing per-base methylation metrics

*.methylKit

`versions_methyldackel`

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

The name of the process

`methyldackel`
`:string`

The name of the tool

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`methyldackel`
`:string`

The name of the tool

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

The expression to obtain the version of the tool

Tools

methyldackel
MIT

Methylation caller from MethylDackel, a (mostly) universal methylation extractor for methyl-seq experiments.

github.com/dpryan79/MethylDackel github.com/dpryan79/MethylDackel/blob/master/README.md

modules/methyldackel_extract

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

Output

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`methylkit`

`meta`
`:map`

`*.methylKit`
`:file`

`versions_methyldackel`

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

`methyldackel`
`:string`

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

Topics

`versions`

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

`methyldackel`
`:string`

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

Tools

methyldackel
MIT

included in

maintainers

get in touch

modules/methyldackel_extract

Description

Input

meta :map

bam :file

bai :file

meta2 :map

fasta :file

fai :file

Output

bedgraph

meta :map

*.bedGraph :file

methylkit

meta :map

*.methylKit :file

versions_methyldackel

${task.process} :string

methyldackel :string

MethylDackel --version 2>&1 | cut -f1 -d' ' :eval

Topics

versions

${task.process} :string

methyldackel :string

MethylDackel --version 2>&1 | cut -f1 -d' ' :eval

Tools

methyldackelMIT

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`methylkit`

`meta`
`:map`

`*.methylKit`
`:file`

`versions_methyldackel`

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

`methyldackel`
`:string`

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

`versions`

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

`methyldackel`
`:string`

`MethylDackel --version 2>&1 | cut -f1 -d' '`
`:eval`

methyldackel
MIT