test: Remove outdated test files and update main test structure for nf-aggregate pipeline.

The test now includes improved assertions and metadata updates for better compatibility with Nextflow versioning.

Author: edmundmiller

modules/local/benchmark_report/nextflow.config

@@ -2,7 +2,7 @@ process {
     withName: 'BENCHMARK_REPORT' {
         publishDir = [
             path: { "${params.outdir}/${metaOut?.projectName?.replace("/", "_") ?: ""}/benchmark_report" },
-            mode: params.publish_dir_mode,
+            mode: 'copy',
             saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.json') ? null : filename }
         ]
         containerOptions = "--user root"

modules/local/plot_run_gantt/nextflow.config

@@ -2,7 +2,7 @@ process {
     withName: 'PLOT_RUN_GANTT' {
         publishDir = [
             path: { "${params.outdir}/${meta.projectName?.replace("/", "_") ?: ""}/gantt" },
-            mode: params.publish_dir_mode,
+            mode: 'copy',
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }

modules/local/seqera_runs_dump/nextflow.config

@@ -6,7 +6,7 @@ process {
         containerOptions = { params.java_truststore_path ? "--volume ${params.java_truststore_path}:${params.java_truststore_path}" : '' }
         publishDir = [
             path: { "${params.outdir}/${metaOut?.projectName?.replace("/", "_") ?: ""}/runs_dump" },
-            mode: params.publish_dir_mode,
+            mode: 'copy',
             saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.json') ? null : filename }
         ]
     }

modules/nf-core/multiqc/nextflow.config

@@ -33,4 +33,4 @@ nextflow_pipeline {
             )
         }
     }
-}
+}