Fix bedtools complement module

software/bedtools/complement/main.nf

@@ -11,7 +11,7 @@ process BEDTOOLS_COMPLEMENT {
         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 {
@@ -19,11 +19,12 @@ process BEDTOOLS_COMPLEMENT {
     }
 
     input:
-    tuple val(meta), path(beds), path(sizes)
+    tuple val(meta), path(bed)
+    path  sizes
 
     output:
-    tuple val(meta), path('*.complement.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 +32,10 @@ process BEDTOOLS_COMPLEMENT {
     """
     bedtools \\
         complement \\
-        -i $beds \\
+        -i $bed \\
         -g $sizes \\
         $options.args \\
-        > ${prefix}.complement.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/complement/meta.yml

@@ -24,22 +24,20 @@ params:
         description: |
             Run the module with Conda using the software specified
             via the `conda` directive
-
 input:
     - meta:
         type: map
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - beds:
+    - bed:
         type: file
-        description: List of bed files
-        pattern: "*.{bed}"
+        description: Input BED file
+        pattern: "*.bed"
     - sizes:
         type: file
         description: File which defines the chromosome lengths for a given genome
-        pattern: "*.{sizes}"
-
+        pattern: "*.sizes"
 output:
     - meta:
         type: map
@@ -49,7 +47,7 @@ output:
     - bed:
         type: file
         description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
-        pattern: "*.{complement.bed}"
+        pattern: "*.bed"
     - version:
         type: file
         description: File containing software version
@@ -57,3 +55,4 @@ output:
 authors:
     -"@Emiller88"
     -"@sruthipsuresh"
+    -"@drpatelh"