modules/modkit_pileup

A bioinformatics tool for working with modified bases

methylationontlong-read

https://github.com/nf-core/modules/[...]/modules/nf-core/modkit/pileup

Description

A bioinformatics tool for working with modified bases

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted BAM/CRAM file

*.{bam,cram}

`bai`
`:file`

Associated index file for BAM. Both BAI and CSI indices are supported by modkit (via htslib).

*.{bai,csi}

`meta2`
`:map`

Groovy Map containing reference information e.g. [ id:'hg38' ]

`fasta`
`:file`

Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering. Note that when using –cpg via ext.args, you must also pass –modified-bases (e.g. ‘–cpg –modified-bases 5mC’) or modkit will error with a missing required argument.

*.fasta

`fai`
`:file`

Associated index file for FASTA

*.fai

`meta3`
`:map`

Groovy Map containing BED file information e.g. [ id:'regions' ]

`bed`
`:file`

BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the file. Must be in BED3 (chr, start, end) or BED6 format; modkit rejects other column counts with “improperly formatted BED line, must be BED3 or BED6” followed by “zero valid positions parsed from BED file”. Note also that modkit requires –motif or –modified-bases in ext.args whenever –include-bed is used, and errors out otherwise.

*.bed

Output

name:type

description

pattern

`bedgz`

`meta`
`:map`

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

`*.bed.gz`
`:file`

bgzf-compressed bedMethyl output file(s)

*.bed

`log`

`meta`
`:map`

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

`*.log`
`:file`

File for debug logs to be written to

*.log

`versions_modkit`

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

The name of the process

`modkit`
`:string`

The name of the tool

`modkit --version | sed 's/modkit //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`modkit`
`:string`

The name of the tool

`modkit --version | sed 's/modkit //'`
`:eval`

The expression to obtain the version of the tool

Tools

modkit
Oxford Nanopore Technologies PLC. Public License Version 1.0

A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data

github.com/nanoporetech/modkit

modules/modkit_pileup

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`meta3`
`:map`

`bed`
`:file`

Output

`bedgz`

`meta`
`:map`

`*.bed.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_modkit`

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

`modkit`
`:string`

`modkit --version | sed 's/modkit //'`
`:eval`

Topics

`versions`

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

`modkit`
`:string`

`modkit --version | sed 's/modkit //'`
`:eval`

Tools

modkit
Oxford Nanopore Technologies PLC. Public License Version 1.0

included in

maintainers

get in touch

modules/modkit_pileup

Description

Input

meta :map

bam :file

bai :file

meta2 :map

fasta :file

fai :file

meta3 :map

bed :file

Output

bedgz

meta :map

*.bed.gz :file

log

meta :map

*.log :file

versions_modkit

${task.process} :string

modkit :string

modkit --version | sed 's/modkit //' :eval

Topics

versions

${task.process} :string

modkit :string

modkit --version | sed 's/modkit //' :eval

Tools

modkitOxford Nanopore Technologies PLC. Public License Version 1.0

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`fai`
`:file`

`meta3`
`:map`

`bed`
`:file`

`bedgz`

`meta`
`:map`

`*.bed.gz`
`:file`

`log`

`meta`
`:map`

`*.log`
`:file`

`versions_modkit`

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

`modkit`
`:string`

`modkit --version | sed 's/modkit //'`
`:eval`

`versions`

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

`modkit`
`:string`

`modkit --version | sed 's/modkit //'`
`:eval`

modkit
Oxford Nanopore Technologies PLC. Public License Version 1.0