All modules corrected, TODO config

software/bedtools/merge/main.nf

@@ -4,6 +4,7 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 def options    = initOptions(params.options)
 
 process BEDTOOLS_MERGE {
+    tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -16,16 +17,16 @@ process BEDTOOLS_MERGE {
     container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
     }
     input:
-        path(sort)
+        tuple val(meta), path(sort)
 
     output:
         path("*.merged.bed"), emit: merge
         path  "*.version.txt", emit: version
-// TODO fix output file naming
     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 merge -i ${sort} ${options.args} > ${prefix}.merged.bed
         bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
         """
 }

tests/software/bedtools/main.nf

@@ -39,14 +39,12 @@ workflow test_bedtools_intersect {
 }
 
 
-//  ensure input file is presorted (uses output of sort module)
+//  TODO use output of sort module
 workflow test_bedtools_merge {
-    test_bedtools_sort()
     def input = []
-    input = [
-        test_bedtools_sort.out.sort.collect { it[1] }.ifEmpty([])
-    ]
-    BEDTOOLS_MERGE(*input)
+    input = [ [ id:'test' ], // meta map
+                file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+    BEDTOOLS_MERGE(input)
 }
 
 // TODO streamline slop module