Add homer

software/homer/annotatepeaks/functions.nf

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+../../lib/functions.nf

software/homer/annotatepeaks/main.nf

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+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '4.11'
+
+process HOMER_ANNOTATEPEAKS {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    container "quay.io/biocontainers/homer:4.11--pl526h9a982cc_2"
+    //container "https://depot.galaxyproject.org/singularity/homer:4.11--pl526h9a982cc_2"
+
+    conda (params.conda ? "bioconda::homer=4.11" : null)
+
+    input:
+    tuple val(meta), path(peak)
+    path fasta
+    path gtf
+    val options
+
+    output:
+    tuple val(meta), path("*annotatePeaks.txt"), emit: txt
+    path "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def ioptions = initOptions(options)
+    def prefix   = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
+    """
+    annotatePeaks.pl \\
+        $peak \\
+        $fasta \\
+        $ioptions.args \\
+        -gtf $gtf \\
+        -cpu $task.cpus \\
+        > ${prefix}.annotatePeaks.txt
+
+    echo $VERSION > ${software}.version.txt
+    """
+}