Bedtools merge adapted to the current module standard

software/bedtools/merge/main.nf

@@ -1,17 +1,32 @@
+def MODULE = "bedtools_merge"
+params.publish_dir = MODULE
+params.publish_results = "default"
+
 process BEDTOOLS_MERGE {
     tag { input_file }
 
+    publishDir "${params.out_dir}/${params.publish_dir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename ->
+                    if (params.publish_results == "none") null
+                    else filename }
+
+    //container "docker.pkg.github.com/nf-core/$MODULE"
     container 'quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0'
 
+    conda "${moduleDir}/environment.yml"
+
     input:
     path (input_file)
     val (bedtools_merge_args)
 
     output:
-    stdout()
+    path "${input_file}.bed", emit: merge
+    path "*.version.txt", emit: version
 
     script:
     """
-    bedtools merge -i ${input_file} ${bedtools_merge_args}
+    bedtools merge -i ${input_file} ${bedtools_merge_args} > ${input_file}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }

software/bedtools/merge/test/input_data/A.bed

@@ -1,5 +0,0 @@
-chr1	951	1061
-chr1	1300	1420
-chr1	1400	1500
-
-

software/bedtools/merge/test/input_data/A.bed

@@ -0,0 +1 @@
+../../../../../tests/data/bed/A.bed

software/bedtools/merge/test/input_data/JK2067_downsampled_s0.1.bam

@@ -0,0 +1 @@
+../../../../../tests/data/bam/JK2067_downsampled_s0.1.bam

software/bedtools/merge/test/main.nf

@@ -2,9 +2,11 @@
 
 nextflow.preview.dsl = 2
 
+params.out_dir = "test_output"
+params.fastqc_args = ''
+params.publish_dir_mode = "copy"
 params.bedtools_merge_args = '' //''-s -c 6 -o distinct'
 
-include check_output from  '../../../../tests/functions/check_process_outputs.nf' // params(params)
 include BEDTOOLS_MERGE from '../main.nf' params(params)
 
 // Define input channels
@@ -14,5 +16,4 @@ ch_input = Channel.fromPath('./input_data/A.bed')
 // Run the workflow
 workflow {
     BEDTOOLS_MERGE(ch_input, params.bedtools_merge_args)
-    // .check_output()
 }