fix bug in assembler argument resolution that may affect test

Author: nschan

nextflow.config

@@ -81,7 +81,7 @@ params {
     // -- Assembly: Flye --
     genome_size                = null // genomesize, optional, can be estimated from ONT reads
     // DEPRECATED: flye_mode                  = '--nano-hq'
-    flye_args                  = "" // extra flye args
+    flye_args                  = '' // extra flye args
     // -- Assembly: hifiasm  --
     hifiasm_args               = '' // extra hifiasm args
     // QC Oriented extra options

subworkflows/local/utils_nfcore_genomeassembler_pipeline/main.nf

@@ -138,6 +138,9 @@ workflow PIPELINE_INITIALISATION {
             def hic_trim        =   !scaffold_hic ? false :
                                     (it.hic_trim ?: params.hic_trim)
 
+            def assembler_ont_args =  it.assembler_ont_args ?: params.assembler_ont_args ?: ''
+            def assembler_hifi_args = it.assembler_hifi_args ?: params.assembler_hifi_args ?: ''
+
 
             // Check if strategy can be inferred
             strategy == "single" && ontreads && hifireads && !((!assembler_ont && assembler_hifi) || (assembler_ont && !assembler_hifi)) ?
@@ -166,13 +169,13 @@ workflow PIPELINE_INITIALISATION {
                     assembler_ont: assembler_ont,
                     assembler_hifi: assembler_hifi,
                     assembly_scaffolding_order: it.assembly_scaffolding_order ?: params.assembly_scaffolding_order ?: "ont_on_hifi",
-                    assembler_ont_args: it.assembler_ont_args ?: params.assembler_ont_args ?:
-                        (assembler_ont == "hifiasm") ? (it.hifiasm_args ?: params.hifiasm_args) :
-                        (assembler_ont == "flye") ? (it.flye_args ?: params.flye_args) :
+                    assembler_ont_args: assembler_ont_args + " " +
+                        (assembler == "flye" && strategy == "single") || (assembler_ont == "flye") ? (it.flye_args ?: params.flye_args) :
+                        (assembler == "hifiasm" && strategy == "single") || (assembler_ont == "hifiasm") ? (it.hifiasm_args ?: params.hifiasm_args) :
                         "",
-                    assembler_hifi_args: it.assembler_hifi_args ?: params.assembler_hifi_args ?:
-                        (assembler_hifi == "hifiasm") ? (it.hifiasm_args ?: params.hifiasm_args) :
-                        (assembler_hifi == "flye") ? (it.flye_args ?: params.flye_args) :
+                    assembler_hifi_args: assembler_hifi_args + " " +
+                        (assembler == "flye" && strategy == "single") || (assembler_hifi == "hifiasm") ? (it.hifiasm_args ?: params.hifiasm_args) :
+                        (assembler == "flye" && strategy == "single") || (assembler_hifi == "flye") ? (it.flye_args ?: params.flye_args) :
                         "",
                     polish: polish,
                     ont_collect: it.ont_collect ?: params.ont_collect,