modules/bedtools_subtract

Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.

bedgffvcfsubtract

https://github.com/nf-core/modules/[...]/modules/nf-core/bedtools/subtract

Description

Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A.

Input

name:type

description

pattern

`meta`
`:map`

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

`intervals1`
`:file`

BED/GFF/VCF

*.{bed|gff|vcf}

`intervals2`
`:file`

BED/GFF/VCF

*.{bed|gff|vcf}

Output

name:type

description

pattern

`bed`

`meta`
`:map`

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

`*.bed`
`:file`

File containing the difference between the two sets of features

`versions_bedtools`

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

The name of the process

`bedtools`
`:string`

The name of the tool

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`bedtools`
`:string`

The name of the tool

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

The expression to obtain the version of the tool

Tools

bedtools
MIT

A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

bedtools.readthedocs.io/en/latest/content/tools/subtract

modules/bedtools_subtract

Description

Input

`meta`
`:map`

`intervals1`
`:file`

`intervals2`
`:file`

Output

`bed`

`meta`
`:map`

`*.bed`
`:file`

`versions_bedtools`

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

`bedtools`
`:string`

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

Topics

`versions`

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

`bedtools`
`:string`

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

Tools

bedtools
MIT

included in

maintainer

get in touch

modules/bedtools_subtract

Description

Input

meta:map

intervals1:file

intervals2:file

Output

bed

meta:map

*.bed:file

versions_bedtools

${task.process}:string

bedtools:string

bedtools --version | sed -e 's/bedtools v//g':eval

Topics

versions

${task.process}:string

bedtools:string

bedtools --version | sed -e 's/bedtools v//g':eval

Tools

bedtools MIT

included in

maintainer

get in touch

`meta`
`:map`

`intervals1`
`:file`

`intervals2`
`:file`

`bed`

`meta`
`:map`

`*.bed`
`:file`

`versions_bedtools`

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

`bedtools`
`:string`

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

`versions`

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

`bedtools`
`:string`

`bedtools --version | sed -e 's/bedtools v//g'`
`:eval`

bedtools
MIT