Very preliminary implementation of passing optional params to bedtools/intersect modules

software/bedtools/intersect/main.nf

@@ -20,12 +20,18 @@ process INTERSECT_BED {
     path (input_file_2)
     val (intersectbed_args)
 
-    output:
-    stdout()
+    //output:
+    //path "${input_file_1.baseName}_i_${input_file_2.baseName}.bed", emit: intersect
+    //path "*.version.txt", emit: version
 
     script:
+    def params_string = intersectbed_args.collect {
+                            /-$it.key $it.value/
+                        } join " "
+
     """
-    bedtools intersect -a ${input_file_1} -b ${input_file_2} ${intersectbed_args}
+    bedtools intersect -a ${input_file_1} -b ${input_file_2} ${params_string} > ${input_file_1.baseName}_i_${input_file_2.baseName}.bed
+    bedtools --version | sed -n "s/.*\\(v.*\$\\)/\\1/p" > bedtools.version.txt
     """
 }
 

software/bedtools/intersect/test/main.nf

@@ -1,7 +1,6 @@
 #!/usr/bin/env nextflow
 
 nextflow.preview.dsl = 2
-
 params.out_dir = "test_output"
 params.fastqc_args = ''
 params.publish_dir_mode = "copy"
@@ -14,7 +13,12 @@ include INTERSECT_BED from '../main.nf' params(params)
 ch_input_1 = Channel.fromPath('./input_data/A.bed')
 ch_input_2 = Channel.fromPath('./input_data/B.bed')
 
+def additional_params_map = [:]
+
+additional_params_map =  [ s: "",
+                           f: 0.9 ]
+
 // Run the workflow
 workflow {
-    INTERSECT_BED(ch_input_1, ch_input_2, params.intersect_args)
+    INTERSECT_BED(ch_input_1, ch_input_2, additional_params_map)
 }