modules/fibertoolsrs_predictm6a

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as)

methylationgenomicsbamm6Anucleosomefiberseq

https://github.com/nf-core/modules/[...]/modules/nf-core/fibertoolsrs/predictm6a

Description

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. Also adds nucleosome (nl, ns) and MTase sensitive patches (al, as)

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted BAM/CRAM file

*.{bam,cram}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

bam file with m6A calls in new/extended MM and ML bam tags

*.bam

`versions_fibertoolsrs`

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

The name of the process

`fibertools-rs`
`:string`

The name of the tool

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`fibertools-rs`
`:string`

The name of the tool

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

The expression to obtain the version of the tool

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_predictm6a

Description

Input

`meta`
`:map`

`bam`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_fibertoolsrs`

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

`fibertools-rs`
`:string`

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

Topics

`versions`

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

`fibertools-rs`
`:string`

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

Tools

fibertoolsrs
MIT

included in

maintainer

get in touch

modules/fibertoolsrs_predictm6a

Description

Input

meta:map

bam:file

Output

bam

meta:map

*.bam:file

versions_fibertoolsrs

${task.process}:string

fibertools-rs:string

ft --version | sed 's/fibertools-rs v//;s/\t.*//':eval

Topics

versions

${task.process}:string

fibertools-rs:string

ft --version | sed 's/fibertools-rs v//;s/\t.*//':eval

Tools

fibertoolsrs MIT

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_fibertoolsrs`

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

`fibertools-rs`
`:string`

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

`versions`

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

`fibertools-rs`
`:string`

`ft --version | sed 's/fibertools-rs v//;s/\t.*//'`
`:eval`

fibertoolsrs
MIT