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`

`versions.yml: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:map

intervals1:file

intervals2:file

Output

bed

meta:map

*.bed:file

versions

versions.yml:file

Tools

bedtools MIT

`meta:map`

`intervals1:file`

`intervals2:file`

`bed`

`meta:map`

`*.bed:file`

`versions`

`versions.yml:file`

bedtools
MIT