modules/fibertoolsrs_extract

Extract Fiber-seq information (such as m6A, CpG, nucleosomes, and MSPs) from BAM file into BED file

methylationgenomicsbamm6Afiberseq

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

Description

Extract Fiber-seq information (such as m6A, CpG, nucleosomes, and MSPs) from BAM file into BED file

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`bam:file`

Sorted BAM/CRAM file

*.{bam,cram}

`extract_type:string`

Type of fiberseq information to extract e.g. m6a, cpg, msp, nuc, all

Output

name:type

description

pattern

`bed`

`meta:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.bed.gz:file`

Gzipped BED file with fiber-seq information

*.bed.gz

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

fibertoolsrs
MIT

Mitchell Vollger's rust tools for fiberseq data.

fiberseq.github.io/fibertools/fibertools https://github.com/fiberseq/fibertools-rs 10.5281/zenodo.14782951

modules/fibertoolsrs_extract

Description

Input

`meta:map`

`bam:file`

`extract_type:string`

Output

`bed`

`meta:map`

`*.bed.gz:file`

`versions`

`versions.yml:file`

Tools

fibertoolsrs
MIT

maintainer

get in touch

modules/fibertoolsrs_extract

Description

Input

meta:map

bam:file

extract_type:string

Output

bed

meta:map

*.bed.gz:file

versions

versions.yml:file

Tools

fibertoolsrs MIT

maintainer

get in touch

`meta:map`

`bam:file`

`extract_type:string`

`bed`

`meta:map`

`*.bed.gz:file`

`versions`

`versions.yml:file`

fibertoolsrs
MIT