Removed arguments from bbmap_reformat_standardise module so they can rather be defined in the config

Author: timrozday-mgnify

modules/ebi-metagenomics/bbmap/reformat_standardise/main.nf

@@ -39,8 +39,6 @@ process BBMAP_REFORMAT_STANDARDISE {
         $interleaved_cmd \\
         $paired_cmd \\
         threads=${task.cpus} \\
-        allowidenticalnames=t \\
-        trimreaddescription=t \\
         ${args} \\
         &> ${prefix}.reformat.sh.log
 

modules/ebi-metagenomics/bbmap/reformat_standardise/tests/main.nf.test

@@ -10,6 +10,8 @@ nextflow_process {
 
     test("paired-end fastq") {
 
+        config "./nextflow.config"
+
         when {
             process {
                 """
@@ -37,6 +39,7 @@ nextflow_process {
     test("paired-end fastq - stub") {
 
         options "-stub"
+        config "./nextflow.config"
 
         when {
             process {

modules/ebi-metagenomics/bbmap/reformat_standardise/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: BBMAP_REFORMAT_STANDARDISE {
+        ext.args = "allowidenticalnames=t trimreaddescription=t"
+    }
+}