Fixed and tested 4 modules, keeping with fastp module syntax

software/bedtools/complement/main.nf

@@ -22,8 +22,8 @@ process BEDTOOLS_COMPLEMENT {
     tuple val(meta), path(beds), path(sizes)
 
     output:
-    tuple val(meta), path("*.complement.bed"), emit: complement
-    path  "*.version.txt"                    , emit: version
+    tuple val(meta), path('*.complement.bed'), emit: bed
+    path  '*.version.txt'                    , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/bedtools/intersect/main.nf

@@ -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('*.intersect.bed'), emit: bed
+    path  '*.version.txt'                   , emit: version
 
     script:
     def software = getSoftwareName(task.process)

software/bedtools/intersect/meta.yml

@@ -1,6 +1,5 @@
 name: bedtools_intersect
 description: allows one to screen for overlaps between two sets of genomic features.
-
 keywords:
     - bed
     - intersect
@@ -51,7 +50,6 @@ output:
         type: file
         description: Overlapped bed file
         pattern: "*.{intersect.bed}"
-
     - version:
         type: file
         description: File containing software version

software/bedtools/merge/main.nf

@@ -13,22 +13,28 @@ process BEDTOOLS_MERGE {
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
-        container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
-    
+
     input:
-        tuple val(meta), path(bed)
+    tuple val(meta), path(beds)
 
     output:
-        path("*.merged.bed"), emit: bed
-        path  "*.version.txt", emit: version
+    tuple val(meta), path('*.merged.bed'), emit: bed
+    path  '*.version.txt'                , emit: version
+
     script:
-        def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        """
-        bedtools merge -i ${sort} ${options.args} > ${prefix}.merged.bed
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
-        """
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedtools \\
+        merge \\
+        -i $beds \\
+        $options.args \\
+        > ${prefix}.merged.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
 }

software/bedtools/merge/meta.yml

@@ -1,6 +1,5 @@
 name: bedtools_merge
 description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
-
 keywords:
     - bed
     - merge
@@ -9,7 +8,6 @@ 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/merge.html
-
 params:
     - outdir:
         type: string
@@ -35,8 +33,9 @@ input:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: List of bed files
+        description: Presorted interval bed file
         pattern: "*.{bed}"
+
 output:
     - meta:
         type: map
@@ -45,14 +44,12 @@ output:
             e.g. [ id:'test', single_end:false ]
     - bed:
         type: file
-        description: Overlapped bed file
+        description: Overlapped bed file with combined features
         pattern: "*.{merged.bed}"
-
     - version:
         type: file
         description: File containing software version
         pattern: "*.{version.txt}"
-
 authors:
     -"@Emiller88"
     -"@sruthipsuresh"

software/bedtools/sort/main.nf

@@ -13,23 +13,28 @@ process BEDTOOLS_SORT {
 
     conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
     } else {
-        container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
+        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
     }
 
     input:
-        tuple val(meta), path(beds)
+    tuple val(meta), path(beds)
 
     output:
-        tuple val(meta), path("*.sort.bed"), emit: bed
-        path  "*.version.txt", emit: version
+    tuple val(meta), path('*.sort.bed'), emit: bed
+    path  '*.version.txt'              , emit: version
 
     script:
-        def software = getSoftwareName(task.process)
-        def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-        """
-        bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
-        """
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedtools \\
+        sort \\
+        -i $beds \\
+        $options.args \\
+        > ${prefix}.sort.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
 }

software/bedtools/sort/meta.yml

@@ -1,6 +1,5 @@
 name: bedtools_sort
 description: Sorts a feature file by chromosome and other criteria.
-
 keywords:
     - bed
     - sort
@@ -9,7 +8,6 @@ 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/sort.html
-
 params:
     - outdir:
         type: string
@@ -33,10 +31,11 @@ input:
         description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-    - bed:
+    - beds:
         type: file
         description: List of bed files
         pattern: "*.{bed}"
+
 output:
     - meta:
         type: map