Corrected pytest and config

.github/workflows/bedtools_merge.yml

@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_merge--symlink --wt 2
+      - run: pytest --tag bedtools_merge --symlink --wt 2

.github/workflows/bedtools_slop.yml

@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_slop--symlink --wt 2
+      - run: pytest --tag bedtools_slop --symlink --wt 2

.github/workflows/bedtools_sort.yml

@@ -37,4 +37,4 @@ jobs:
         run: python -m pip install --upgrade pip pytest-workflow
 
       # Test the module
-      - run: pytest --tag bedtools_sort--symlink --wt 2
+      - run: pytest --tag bedtools_sort --symlink --wt 2

software/bedtools/complement/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bedtools/complement/main.nf

@@ -16,7 +16,7 @@ process BEDTOOLS_COMPLEMENT {
     } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
-    
+
     input:
         tuple val(meta), path(beds), path (sizes)
 

software/bedtools/genomecov/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bedtools/intersect/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bedtools/intersect/main.nf

@@ -9,7 +9,7 @@ process BEDTOOLS_INTERSECT {
     publishDir "${params.outdir}",
         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 =2.29.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
         container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0"

software/bedtools/merge/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bedtools/slop/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}

software/bedtools/slop/main.nf

@@ -16,7 +16,7 @@ process BEDTOOLS_SLOP {
     } else {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
-    
+
 
     input:
         tuple val(meta), path(beds), path (sizes)
@@ -42,6 +42,6 @@ process BEDTOOLS_SLOP {
         """
         slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
-        """       
+        """
         }
 }

software/bedtools/sort/functions.nf

@@ -56,4 +56,4 @@ def saveFiles(Map args) {
             return "${getPathFromList(path_list)}/$args.filename"
         }
     }
-}
+}