feat(homer): Add pos2bed module (#1435)

* feat(homer): Add pos2bed module

* test(homer): Pass bed format

* test(homer): Add upstream dependencies to avoid regressions

* Update modules/homer/pos2bed/main.nf

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
This commit is contained in:
Edmund Miller 2022-03-25 08:29:36 -05:00 committed by GitHub
parent 3d31fa4d04
commit 98ed71c8f6
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6 changed files with 119 additions and 0 deletions

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@ -0,0 +1,33 @@
def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_POS2BED {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::homer=4.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(peaks)
output:
tuple val(meta), path("*.bed"), emit: bed
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
pos2bed.pl $peaks > ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
homer: $VERSION
END_VERSIONS
"""
}

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@ -0,0 +1,42 @@
name: "homer_pos2bed"
description: Coverting from HOMER peak to BED file formats
keywords:
- peaks
tools:
- "homer":
description: |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
homepage: "http://homer.ucsd.edu/homer/index.html"
documentation: "http://homer.ucsd.edu/homer/"
tool_dev_url: "http://homer.ucsd.edu/homer/ngs/miscellaneous.html"
doi: 10.1016/j.molcel.2010.05.004.
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- tagDir:
type: directory
description: "The 'Tag Directory'"
pattern: "tagDir"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: BED file
pattern: "*.bed"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"

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@ -887,6 +887,12 @@ homer/makeucscfile:
- modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/**
homer/pos2bed:
- modules/homer/pos2bed/**
- modules/homer/maketagdirectory/**
- modules/homer/findpeaks/**
- tests/modules/homer/pos2bed/**
hpsuissero:
- modules/hpsuissero/**
- tests/modules/hpsuissero/**

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@ -0,0 +1,19 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf'
include { HOMER_POS2BED } from '../../../../modules/homer/pos2bed/main.nf'
workflow test_homer_pos2bed {
input = [[id:'test'],
[file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
HOMER_MAKETAGDIRECTORY (input, fasta)
HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
}

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@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: HOMER_MAKETAGDIRECTORY {
ext.args = '-format bed'
}
}

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@ -0,0 +1,10 @@
- name: "homer pos2bed"
command: nextflow run ./tests/modules/homer/pos2bed -entry test_homer_pos2bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/pos2bed/nextflow.config
tags:
- "homer"
- "homer/pos2bed"
files:
- path: "output/homer/test.bed"
md5sum: 0b9ebd8f06b9c820a551fbdb2d7635ee
- path: output/homer/versions.yml
md5sum: 1485f4b2d76484e8fe3310e2505de2fd