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:false ]

bam:file

BAM/BED/SAM file

*.{bam,bed,sam}

fasta:file

Fasta file of reference genome

*.fasta

Output

name:type
description
pattern

tagdir

meta:map

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

*_tagdir:directory

The “Tag Directory”

*_tagdir

taginfo

meta:map

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

*_tagdir/tagInfo.txt:directory

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

*_tagdir/tagInfo.txt

versions

versions.yml: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.

http://homer.ucsd.edu/homer 10.1016/j.molcel.2010.05.004.

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.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352

DESeq2
LGPL-3.0-or-later

Differential gene expression analysis based on the negative binomial distribution

bioconductor.org/packages/DESeq2 https://github.com/mikelove/DESeq2 10.18129/B9.bioc.DESeq2
nascent
Github user edmundmiller
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