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>

modules/homer/pos2bed/main.nf

@@ -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
+    """
+}

modules/homer/pos2bed/meta.yml

@@ -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"

tests/config/pytest_modules.yml

@@ -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/**

tests/modules/homer/pos2bed/main.nf

@@ -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 )
+}

tests/modules/homer/pos2bed/nextflow.config

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

tests/modules/homer/pos2bed/test.yml

@@ -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