Description

For each feature in A, finds the closest feature (upstream or downstream) in B.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input_1 (file)

The file to find the closest features of

*.{bed,vcf,gff}(.gz)?

input_2 (file(s))

The input file(s) to find the closest features from

*.{bed,vcf,gff}(.gz)?

fasta_fai (file)

The index of the FASTA reference. Needed when the argument --sorted is used

*.fai

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

output (file)

The resulting BED file containing the closest features

*.{bed,vcf,gff}
author
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

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/closest