From f61ad7506ad7b3c84daefc052077e1bf5aeac194 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Aug 2020 17:16:56 +0100
Subject: [PATCH] Add homer

---
 software/homer/annotatepeaks/functions.nf |  1 +
 software/homer/annotatepeaks/main.nf      | 43 +++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 120000 software/homer/annotatepeaks/functions.nf
 create mode 100644 software/homer/annotatepeaks/main.nf

diff --git a/software/homer/annotatepeaks/functions.nf b/software/homer/annotatepeaks/functions.nf
new file mode 120000
index 00000000..5e1a8e03
--- /dev/null
+++ b/software/homer/annotatepeaks/functions.nf
@@ -0,0 +1 @@
+../../lib/functions.nf
\ No newline at end of file
diff --git a/software/homer/annotatepeaks/main.nf b/software/homer/annotatepeaks/main.nf
new file mode 100644
index 00000000..496f5cc4
--- /dev/null
+++ b/software/homer/annotatepeaks/main.nf
@@ -0,0 +1,43 @@
+// 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
+    """
+}