Fix quoting and undercore unused variables

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#724](https://github.com/nf-core/mag/pull/724) - Fix quoting in `utils_nfcore_mag_pipeline/main.nf` (added by @dialvarezs)
 - [#716](https://github.com/nf-core/mag/pull/692) - Make short read processing a subworkflow (added by @muabnezor)
 - [#708](https://github.com/nf-core/mag/pull/708) - Fixed channel passed as GUNC input (added by @dialvarezs)
 

README.md

@@ -90,6 +90,7 @@ Other code contributors include:
 - [Phil Palmer](https://github.com/PhilPalmer)
 - [@willros](https://github.com/willros)
 - [Adam Rosenbaum](https://github.com/muabnezor)
+- [Diego Alvarez](https://github.com/dialvarezs)
 
 Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)
 

subworkflows/local/utils_nfcore_mag_pipeline/main.nf

@@ -26,7 +26,7 @@ workflow PIPELINE_INITIALISATION {
     take:
     version           // boolean: Display version and exit
     validate_params   // boolean: Boolean whether to validate parameters against the schema at runtime
-    monochrome_logs   // boolean: Do not use coloured log outputs
+    _monochrome_logs  // boolean: Do not use coloured log outputs
     nextflow_cli_args //   array: List of positional nextflow CLI args
     outdir            //  string: The output directory where the results will be saved
     input             //  string: Path to input samplesheet
@@ -71,13 +71,13 @@ workflow PIPELINE_INITIALISATION {
 
     // Validate FASTQ input
     ch_samplesheet = Channel
-        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
+        .fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
         .map {
             validateInputSamplesheet(it[0], it[1], it[2], it[3])
         }
 
     // Prepare FASTQs channel and separate short and long reads and prepare
-    ch_raw_short_reads = ch_samplesheet.map { meta, sr1, sr2, lr ->
+    ch_raw_short_reads = ch_samplesheet.map { meta, sr1, sr2, _lr ->
         meta.run = meta.run == [] ? "0" : meta.run
         meta.single_end = params.single_end
 
@@ -89,7 +89,7 @@ workflow PIPELINE_INITIALISATION {
         }
     }
 
-    ch_raw_long_reads = ch_samplesheet.map { meta, sr1, sr2, lr ->
+    ch_raw_long_reads = ch_samplesheet.map { meta, _sr1, _sr2, lr ->
         if (lr) {
             meta.run = meta.run == [] ? "0" : meta.run
             return [meta, lr]
@@ -129,13 +129,13 @@ workflow PIPELINE_INITIALISATION {
     // Cross validation of input assembly and read IDs: ensure groups are all represented between reads and assemblies
     if (params.assembly_input) {
         ch_read_ids = ch_samplesheet
-            .map { meta, sr1, sr2, lr -> params.coassemble_group ? meta.group : meta.id }
+            .map { meta, _sr1, _sr2, _lr -> params.coassemble_group ? meta.group : meta.id }
             .unique()
             .toList()
             .sort()
 
         ch_assembly_ids = ch_input_assemblies
-            .map { meta, fasta -> params.coassemble_group ? meta.group : meta.id }
+            .map { meta, _fasta -> params.coassemble_group ? meta.group : meta.id }
             .unique()
             .toList()
             .sort()
@@ -286,14 +286,14 @@ def validateInputParameters(hybrid) {
 
     // Check if BUSCO parameters combinations are valid
     if (params.skip_binqc && params.binqc_tool == 'checkm') {
-        error('[nf-core/mag] ERROR: Both --skip_binqc and --binqc_tool 'checkm' are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool.')
+        error("[nf-core/mag] ERROR: Both --skip_binqc and --binqc_tool 'checkm' are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool.")
     }
     if (params.skip_binqc) {
         if (params.busco_db) {
-            error('[nf-core/mag] ERROR: Both --skip_binqc and --busco_db are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool 'busco' with --busco_db.')
+            error("[nf-core/mag] ERROR: Both --skip_binqc and --busco_db are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool 'busco' with --busco_db.")
         }
         if (params.busco_auto_lineage_prok) {
-            error('[nf-core/mag] ERROR: Both --skip_binqc and --busco_auto_lineage_prok are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool 'busco' with --busco_auto_lineage_prok.')
+            error("[nf-core/mag] ERROR: Both --skip_binqc and --busco_auto_lineage_prok are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool 'busco' with --busco_auto_lineage_prok.")
         }
     }