Fix bedtools slip module

software/bedtools/slop/main.nf

@@ -11,20 +11,20 @@ process BEDTOOLS_SLOP {
         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 {
         container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
 
-
     input:
-    tuple val(meta), path(beds), path (sizes)
+    tuple val(meta), path(bed)
+    path  sizes
 
     output:
-    tuple val(meta), path("*.slop.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)
@@ -32,10 +32,10 @@ process BEDTOOLS_SLOP {
     """
     bedtools \\
         slop \\
-        -i $beds \\
+        -i $bed \\
         -g $sizes \\
         $options.args \\
-        > ${prefix}.slop.bed
+        > ${prefix}.bed
 
     bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
     """

software/bedtools/slop/meta.yml

@@ -1,75 +1,59 @@
 name: bedtools_slop
 description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
 keywords:
-  - bed
-  - slopBed
+    - bed
+    - slopBed
 tools:
-  - bedtools:
-      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/slop.html
-
+    - bedtools:
+        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/slop.html
 params:
-  - l:
-      type: integer
-      description: The number of base pairs to subtract from the start coordinate
-  - r:
-      type: integer
-      description: The number of base pairs to add to the end coordinate
-  - b:
-      type: integer
-      description: Increases the entry by the same number base pairs in each direction
-  - pct:
-      type: boolean
-      description: |
-        Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.
-
-  - header:
-      type: boolean
-      description: |
-        Print the header from the input file prior to results.
-
-  - outdir:
-      type: string
-      description: |
-        The pipeline's output directory. By default, the module will
-        output files into `$params.outdir/<SOFTWARE>`
-  - publish_dir_mode:
-      type: string
-      description: |
-        Value for the Nextflow `publishDir` mode parameter.
-        Available: symlink, rellink, link, copy, copyNoFollow, move.
-  - enable_conda:
-      type: boolean
-      description: |
-        Run the module with Conda using the software specified
-        via the `conda` directive
-
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        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
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bed:
-      type: file
-      description: List of bed files
-      pattern: "*.{bed}"
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Input BED file
+        pattern: "*.{bed}"
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - bed:
-      type: file
-      description: Edited bed file
-      pattern: "*.{slop.bed}"
-
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-
-authors: -"@Emiller88"
-  -"@sruthipsuresh"
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Slopped BED file
+        pattern: "*.{bed}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors: 
+    - "@Emiller88"
+    - "@sruthipsuresh"
+    - "@drpatelh"

tests/software/bedtools/slop/main.nf

@@ -7,9 +7,8 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP
 workflow test_bedtools_slop {
     def input = []
     input = [ [ id:'test'],
-              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
-              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ]
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
 
-    BEDTOOLS_SLOP( input )
+    BEDTOOLS_SLOP ( input, file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) )
 }
 

tests/software/bedtools/slop/test.yml

@@ -4,5 +4,5 @@
     - bedtools
     - bedtools_slop
   files:
-    - path: output/bedtools/test.slop.bed
+    - path: output/bedtools/test.bed
       md5sum: 5f6ecc3e3cc6cee9537a1d088b02abec