updated test file and main.nf file

software/bedtools/slopRefseq/functions.nf

@@ -1,59 +0,0 @@
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/bedtools/sloprefseq/main.nf

@@ -21,8 +21,8 @@ process BEDTOOLS_SLOPREFSEQ {
     }
 
     input:
-        path sizes 
         tuple val(meta), path(beds)
+        path  sizes
 
     output:
         tuple val(meta), path("*.sloprefseq.bed"), emit: bed
@@ -33,7 +33,7 @@ process BEDTOOLS_SLOPREFSEQ {
         def beds_files = beds.sort()
         def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
         """
-        slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
+        slopBed -i ln -s ${beds[0]} -g ln -s $sizes -l ${params.upstream} -r ${params.downstream} > ${prefix}.sloprefseq.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

software/bedtools/sloprefseq/test/main.nf

@@ -10,10 +10,13 @@ include { BEDTOOLS_SLOPREFSEQ } from '../../sloprefseq/main.nf' addParams( optio
 workflow test_bed_file{
     def input = []
     input = [ [ id:'test', single_end:true ], 
-              [ file("${baseDir}/input/A.bed", checkIfExists: true),
+              [ file("${baseDir}/input/A.bed", checkIfExists: true),] ]
-                file("${baseDir}/input/genome.sizes", checkIfExists: true) ] ]
 
-    BEDTOOLS_SLOPREFSEQ ( input, [ publish_dir:'test_bed_file' ] )
+    BEDTOOLS_SLOPREFSEQ (
+        input, 
+        file("${baseDir}/input/genome.sizes", checkIfExists: true)
+    )
+    
 
 }
 

software/bedtools/sloprefseq/test/nextflow.config

@@ -1,3 +1,4 @@
+  
 params {
     outdir = "output/"
     publish_dir_mode = "copy"

software/bedtools/sloprefseq/test_main.nf

@@ -1,19 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.preview.dsl = 2
-params.out_dir = "test_output"
-params.upstream = 1
-params.downstream = 10
-
-include BEDTOOLS_SLOPEREFSEQ from '../main.nf' params(params)
-
-// Define input channels
-ch_input_1 = Channel.fromPath('./tests/data/bed/A.bed')
-ch_input_2 = Channel.fromPath('./tests/data/bed/genome.sizes')
-
-def additional_params_map = [:]
-
-// Run the workflow
-workflow {
-    BEDTOOLS_SLOPEREFSEQ(ch_input_1, ch_input_2, additional_params_map)
-}