From 38964ecfc0aa9c23f4208f11616ca4ef4e58ddf8 Mon Sep 17 00:00:00 2001
From: drpatelh <drhpatel@gmail.com>
Date: Sun, 7 Feb 2021 21:32:01 +0000
Subject: [PATCH] Fix bedtools intersect module

---
 software/bedtools/intersect/main.nf        | 12 ++++++------
 software/bedtools/intersect/meta.yml       | 20 ++++++++++++--------
 tests/software/bedtools/intersect/main.nf  |  2 +-
 tests/software/bedtools/intersect/test.yml |  2 +-
 4 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/software/bedtools/intersect/main.nf b/software/bedtools/intersect/main.nf
index c8db70d2..77283760 100644
--- a/software/bedtools/intersect/main.nf
+++ b/software/bedtools/intersect/main.nf
@@ -11,7 +11,7 @@ process BEDTOOLS_INTERSECT {
         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=2.30.0" : null)
+    conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
@@ -22,8 +22,8 @@ process BEDTOOLS_INTERSECT {
     tuple val(meta), path(bed1), path(bed2)
 
     output:
-    tuple val(meta), path('*.intersect.bed'), emit: bed
-    path  '*.version.txt'                   , emit: version
+    tuple val(meta), path('*.bed'), emit: bed
+    path  '*.version.txt'         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -31,10 +31,10 @@ process BEDTOOLS_INTERSECT {
     """
     bedtools \\
         intersect \\
-        -a ${bed1} \\
-        -b ${bed2} \\
+        -a $bed1 \\
+        -b $bed2 \\
         $options.args \\
-        > ${prefix}.intersect.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """
diff --git a/software/bedtools/intersect/meta.yml b/software/bedtools/intersect/meta.yml
index 34e00e45..5a72df53 100644
--- a/software/bedtools/intersect/meta.yml
+++ b/software/bedtools/intersect/meta.yml
@@ -24,7 +24,11 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
 input:
     - meta:
         type: map
@@ -33,13 +37,12 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed1:
         type: file
-        description: Bed file, each feature in 1 is compared to 2 in search of overlaps
+        description: BED file, each feature in 1 is compared to 2 in search of overlaps
         pattern: "*.{bed}"
     - bed2:
         type: file
-        description: Second bed file, used to compare to 1.
+        description: Second bed file, used to compare to first BED file
         pattern: "*.{bed}"
-
 output:
     - meta:
         type: map
@@ -48,12 +51,13 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Overlapped bed file
-        pattern: "*.{intersect.bed}"
+        description: BED file with intersected intervals
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    -"@Emiller88"
-    -"@sruthipsuresh"
+    - "@Emiller88"
+    - "@sruthipsuresh"
+    - "@drpatelh"
diff --git a/tests/software/bedtools/intersect/main.nf b/tests/software/bedtools/intersect/main.nf
index 83635419..5bbca7e8 100644
--- a/tests/software/bedtools/intersect/main.nf
+++ b/tests/software/bedtools/intersect/main.nf
@@ -10,5 +10,5 @@ workflow test_bedtools_intersect {
               file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
               file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ]
 
-    BEDTOOLS_INTERSECT( input )
+    BEDTOOLS_INTERSECT ( input )
 }
diff --git a/tests/software/bedtools/intersect/test.yml b/tests/software/bedtools/intersect/test.yml
index fe60d7ca..5d5d3711 100644
--- a/tests/software/bedtools/intersect/test.yml
+++ b/tests/software/bedtools/intersect/test.yml
@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_intersect
   files:
-    - path: output/bedtools/test.intersect.bed
+    - path: output/bedtools/test.bed
       md5sum: cc1bb317886e7df0a942b56f8a320d9c