From 29639c522fdddadf5f8b61015b3a9f6452d749aa Mon Sep 17 00:00:00 2001
From: sruthipsuresh <sruthiprabhasuresh@gmail.com>
Date: Fri, 8 Jan 2021 13:54:56 -0600
Subject: [PATCH] Corrected sort

---
 software/bedtools/sort/main.nf  | 4 ++--
 tests/software/bedtools/main.nf | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/software/bedtools/sort/main.nf b/software/bedtools/sort/main.nf
index 3c490131..9ff7fda9 100644
--- a/software/bedtools/sort/main.nf
+++ b/software/bedtools/sort/main.nf
@@ -21,14 +21,14 @@ process BEDTOOLS_SORT {
         tuple val(meta), path(beds)
 
     output:
-        tuple val(meta), path("*.sort"), emit: sort
+        tuple val(meta), path("*.sort.bed"), emit: sort
         path  "*.version.txt", emit: version
 
     script:
         def software = getSoftwareName(task.process)
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        bedtools sort -i $beds ${options.args} > ${prefix}.sort
+        bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }
diff --git a/tests/software/bedtools/main.nf b/tests/software/bedtools/main.nf
index dd71b960..611f2b8c 100644
--- a/tests/software/bedtools/main.nf
+++ b/tests/software/bedtools/main.nf
@@ -77,6 +77,7 @@ workflow test_bedtools_sort {
               file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
     BEDTOOLS_SORT( input )
+
 }