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{:bash}`
`:map`

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

`intervals1{:bash}`
`:file`

BED/GFF/VCF

*.{bed|gff|vcf}

`intervals2{:bash}`
`:file`

BED/GFF/VCF

*.{bed|gff|vcf}

Output

name:type

description

pattern

`bed{:bash}`

`meta{:bash}`
`:map`

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

`*.bed{:bash}`
`:file`

File containing the difference between the two sets of features

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

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{:bash}`
`:map`

`intervals1{:bash}`
`:file`

`intervals2{:bash}`
`:file`

Output

`bed{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

bedtools
MIT

included in

maintainer

get in touch

modules/bedtools_subtract

Description

Input

meta{:bash}:map

intervals1{:bash}:file

intervals2{:bash}:file

Output

bed{:bash}

meta{:bash}:map

*.bed{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

bedtools MIT

included in

maintainer

get in touch

`meta{:bash}`
`:map`

`intervals1{:bash}`
`:file`

`intervals2{:bash}`
`:file`

`bed{:bash}`

`meta{:bash}`
`:map`

`*.bed{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

bedtools
MIT