Fix bedtools merge module

software/bedtools/merge/main.nf

@@ -9,9 +9,9 @@ process BEDTOOLS_MERGE {
     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:'') }
+        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 {
@@ -19,11 +19,11 @@ process BEDTOOLS_MERGE {
     }
 
     input:
-    tuple val(meta), path(beds)
+    tuple val(meta), path(bed)
 
     output:
-    tuple val(meta), path('*.merged.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)
@@ -31,9 +31,9 @@ process BEDTOOLS_MERGE {
     """
     bedtools \\
         merge \\
-        -i $beds \\
+        -i $bed \\
         $options.args \\
-        > ${prefix}.merged.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/merge/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
@@ -33,9 +37,8 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Presorted interval bed file
+        description: Input BED file
         pattern: "*.{bed}"
-
 output:
     - meta:
         type: map
@@ -45,11 +48,12 @@ output:
     - bed:
         type: file
         description: Overlapped bed file with combined features
-        pattern: "*.{merged.bed}"
+        pattern: "*.{bed}"
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
-    -"@Emiller88"
-    -"@sruthipsuresh"
+    - "@Emiller88"
+    - "@sruthipsuresh"
+    - "@drpatelh"

tests/software/bedtools/merge/main.nf

@@ -9,6 +9,6 @@ workflow test_bedtools_merge {
     input = [ [ id:'test'],
               file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
-    BEDTOOLS_MERGE( input )
+    BEDTOOLS_MERGE ( input )
 }
 

tests/software/bedtools/merge/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_merge
   files:
-    - path: output/bedtools/test.merged.bed
+    - path: output/bedtools/test.bed
       md5sum: 13e5a3b254fac35fe0da0c92cbaf1761