From 898c0775c6ce160ec5a5b4057c98f83055424612 Mon Sep 17 00:00:00 2001
From: sruthipsuresh <58604926+sruthipsuresh@users.noreply.github.com>
Date: Fri, 30 Oct 2020 08:55:42 -0500
Subject: [PATCH] Main.nf for bedtools module added.

---
 software/bedtools/fixbedcoordinates/main.nf | 41 +++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 software/bedtools/fixbedcoordinates/main.nf

diff --git a/software/bedtools/fixbedcoordinates/main.nf b/software/bedtools/fixbedcoordinates/main.nf
new file mode 100644
index 00000000..a7f1e5ec
--- /dev/null
+++ b/software/bedtools/fixbedcoordinates/main.nf
@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+def VERSION = '2.29'
+
+process BEDTOOLS_FIXBEDCOORDINATES {
+    tag "$meta.id"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 "
+    } else {
+        container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
+    }
+
+    input:
+        tuple val(meta), path("*.sloprefseq.bed")
+
+    output:
+        tuple val(meta), path("*.sloprefseqsorted.bed"), emit: bed
+        path  "*.version.txt", emit: version
+
+    script:
+        def software = getSoftwareName(task.process)
+        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+        // sorted via chromosome, then by start position
+        """
+         awk -F '\\t' 'length($1) <= 5 {{ print }}' ${prefix}.sloprefseq.bed |
+         awk '{{ if ($2 > $3) {{ t = $2; $2 = $3; $3 = t; }} \
+         else if ($2 == $3) {{ $3 += 1; }} print $0; }}' OFS='\\t' - \
+         | sort-bed > ${prefix}.sloprefseqsorted.bed
+         echo $VERSION > ${software}.version.txt
+        """
+}