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}

`meta2`
`:map`

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

`bai`
`:file`

BAM/CRAM index file

*.{bai,crai}

`meta3`
`:map`

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

`fasta`
`:file`

Input genome fasta file

*.{fasta,fa}

`meta4`
`:map`

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

`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`

`versions.yml`
`:file`

File containing software versions

versions.yml

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`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

Output

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`methylkit`

`meta`
`:map`

`*.methylKit`
`:file`

`versions`

`versions.yml`
`:file`

Tools

methyldackel
MIT

included in

maintainers

get in touch

modules/methyldackel_extract

Description

Input

meta:map

bam:file

meta2:map

bai:file

meta3:map

fasta:file

meta4:map

fai:file

Output

bedgraph

meta:map

*.bedGraph:file

methylkit

meta:map

*.methylKit:file

versions

versions.yml:file

Tools

methyldackel MIT

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`bai`
`:file`

`meta3`
`:map`

`fasta`
`:file`

`meta4`
`:map`

`fai`
`:file`

`bedgraph`

`meta`
`:map`

`*.bedGraph`
`:file`

`methylkit`

`meta`
`:map`

`*.methylKit`
`:file`

`versions`

`versions.yml`
`:file`

methyldackel
MIT