Description

Create a tag directory with the HOMER suite

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/BED/SAM file

*.{bam,bed,sam}

fasta (file)

Fasta file of reference genome

*.fasta

Output

Name (Type)
Description
Pattern

meta (map)

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

]

tagdir (directory)

The “Tag Directory”

*_tagdir

taginfo (directory)

The tagInfo.txt included to ensure there’s proper output

*_tagdir/tagInfo.txt

versions (file)

File containing software versions

versions.yml

Tools

homer
GPL-3.0-or-later

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

samtools
MIT

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

DESeq2
LGPL-3.0-or-later

Differential gene expression analysis based on the negative binomial distribution