Fix bedtools genomecov module

software/bedtools/genomecov/main.nf

@@ -11,7 +11,7 @@ process BEDTOOLS_GENOMECOV {
         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 {
@@ -19,10 +19,10 @@ process BEDTOOLS_GENOMECOV {
     }
 
     input:
-    tuple val(meta), path(bams)
+    tuple val(meta), path(bam)
 
     output:
-    tuple val(meta), path("*.bed"), emit: coverage
+    tuple val(meta), path("*.bed"), emit: bed
     path  "*.version.txt"         , emit: version
 
     script:
@@ -31,7 +31,7 @@ process BEDTOOLS_GENOMECOV {
     """
     bedtools \\
         genomecov \\
-        -ibam $bams \\
+        -ibam $bam \\
         $options.args \\
         > ${prefix}.bed
 

software/bedtools/genomecov/meta.yml

@@ -9,7 +9,6 @@ tools:
         description: |
             A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
         documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
-
 params:
     - outdir:
         type: string
@@ -26,7 +25,11 @@ 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
@@ -35,7 +38,7 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bam:
         type: file
-        description: List of bam files
+        description: Input BAM file
         pattern: "*.{bam}"
 output:
     - meta:
@@ -47,12 +50,11 @@ output:
         type: file
         description: Computed genomecov bed file
         pattern: "*.{bed}"
-
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"
+    - "@drpatelh"

tests/software/bedtools/genomecov/main.nf

@@ -4,7 +4,6 @@ nextflow.enable.dsl = 2
 
 include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
 
-
 workflow test_bedtools_genomecov {
     def input = []
     input = [ [ id:'test'],