From 6fe4ec16df1e45221de2e61f301638b4b5d7bd02 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Wed, 5 Aug 2020 17:16:23 +0100
Subject: [PATCH] Add ucsc

---
 software/ucsc/bedgraphtobigwig/functions.nf |  1 +
 software/ucsc/bedgraphtobigwig/main.nf      | 35 +++++++++++++++++++++
 2 files changed, 36 insertions(+)
 create mode 120000 software/ucsc/bedgraphtobigwig/functions.nf
 create mode 100644 software/ucsc/bedgraphtobigwig/main.nf

diff --git a/software/ucsc/bedgraphtobigwig/functions.nf b/software/ucsc/bedgraphtobigwig/functions.nf
new file mode 120000
index 00000000..5e1a8e03
--- /dev/null
+++ b/software/ucsc/bedgraphtobigwig/functions.nf
@@ -0,0 +1 @@
+../../lib/functions.nf
\ No newline at end of file
diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf
new file mode 100644
index 00000000..4da63fe1
--- /dev/null
+++ b/software/ucsc/bedgraphtobigwig/main.nf
@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+def VERSION = '377'
+
+process UCSC_BEDRAPHTOBIGWIG {
+    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/ucsc-bedgraphtobigwig:377--h446ed27_1"
+    //container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1"
+
+    conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
+
+    input:
+    tuple val(meta), path(bedgraph)
+    path sizes
+    val options
+
+    output:
+    tuple val(meta), path("*.bigWig"), emit: bigwig
+    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}"
+    """
+    bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig
+    echo $VERSION > ${software}.version.txt
+    """
+}