modules/homer_maketagdirectory

Create a tag directory with the HOMER suite

peaksbedbamsam

https://github.com/nf-core/modules/[...]/modules/nf-core/homer/maketagdirectory

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_homer`

`${task.process}`
`:string`

The name of the process

`homer`
`:string`

The name of the tool

`4.11`
`:string`

The expression to obtain the version of the tool

`versions_samtools`

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version 2>&1 | sed '1!d;s/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

`versions_deseq2`

`${task.process}`
`:string`

The name of the process

`deseq2`
`:string`

The name of the tool

`Rscript -e "cat(as.character(packageVersion('DESeq2')))"`
`:eval`

The expression to obtain the version of the tool

`versions_edger`

`${task.process}`
`:string`

The name of the process

`edger`
`:string`

The name of the tool

`Rscript -e "cat(as.character(packageVersion('edgeR')))"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`homer`
`:string`

The name of the tool

`4.11`
`:string`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version 2>&1 | sed '1!d;s/^.*samtools //'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`deseq2`
`:string`

The name of the tool

`Rscript -e "cat(as.character(packageVersion('DESeq2')))"`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`edger`
`:string`

The name of the tool

`Rscript -e "cat(as.character(packageVersion('edgeR')))"`
`:eval`

The expression to obtain the version of the tool

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

edgeR
GPL >=2

Empirical Analysis of Digital Gene Expression Data in R

bioinf.wehi.edu.au/edgeR bioconductor.org/packages/edgeR https://git.bioconductor.org/packages/edgeR 10.18129/B9.bioc.edgeR

modules/homer_maketagdirectory

Description

Input

meta:map

bam:file

fasta:file

Output

tagdir

meta:map

*_tagdir:directory

taginfo

meta:map

*_tagdir/tagInfo.txt:directory

versions_homer

${task.process}:string

homer:string

4.11:string

versions_samtools

${task.process}:string

samtools:string

samtools --version 2>&1 | sed '1!d;s/^.*samtools //':eval

versions_deseq2

${task.process}:string

deseq2:string

Rscript -e "cat(as.character(packageVersion('DESeq2')))":eval

versions_edger

${task.process}:string

edger:string

Rscript -e "cat(as.character(packageVersion('edgeR')))":eval

Topics

versions

${task.process}:string

homer:string

4.11:string

${task.process}:string

samtools:string

samtools --version 2>&1 | sed '1!d;s/^.*samtools //':eval

${task.process}:string

deseq2:string

Rscript -e "cat(as.character(packageVersion('DESeq2')))":eval

${task.process}:string

edger:string

Rscript -e "cat(as.character(packageVersion('edgeR')))":eval

Tools

homer GPL-3.0-or-later

samtools MIT

DESeq2 LGPL-3.0-or-later

edgeR GPL >=2

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`fasta`
`:file`

`tagdir`

`meta`
`:map`

`*_tagdir`
`:directory`

`taginfo`

`meta`
`:map`

`*_tagdir/tagInfo.txt`
`:directory`

`versions_homer`

`${task.process}`
`:string`

`homer`
`:string`

`4.11`
`:string`

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version 2>&1 | sed '1!d;s/^.*samtools //'`
`:eval`

`versions_deseq2`

`${task.process}`
`:string`

`deseq2`
`:string`

`Rscript -e "cat(as.character(packageVersion('DESeq2')))"`
`:eval`

`versions_edger`

`${task.process}`
`:string`

`edger`
`:string`

`Rscript -e "cat(as.character(packageVersion('edgeR')))"`
`:eval`

`versions`

`${task.process}`
`:string`

`homer`
`:string`

`4.11`
`:string`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools --version 2>&1 | sed '1!d;s/^.*samtools //'`
`:eval`

`${task.process}`
`:string`

`deseq2`
`:string`

`Rscript -e "cat(as.character(packageVersion('DESeq2')))"`
`:eval`

`${task.process}`
`:string`

`edger`
`:string`

`Rscript -e "cat(as.character(packageVersion('edgeR')))"`
`:eval`

homer
GPL-3.0-or-later

samtools
MIT

DESeq2
LGPL-3.0-or-later

edgeR
GPL >=2