Changes in module 'nf-core/modules/bases2fastq'
--- modules/nf-core/bases2fastq/main.nf
+++ modules/nf-core/bases2fastq/main.nf
@@ -11,14 +11,19 @@
     tuple val(meta), path(run_manifest), path(run_dir)
 
     output:
-    tuple val(meta), path('output/Samples/*/*_R*.fastq.gz'), emit: sample_fastq
-    tuple val(meta), path('output/Samples/*/*.json')       , emit: sample_json
-    tuple val(meta), path('output/*.html')                 , emit: qc_report
-    tuple val(meta), path('output/RunStats.json')          , emit: run_stats
-    tuple val(meta), path('output/RunManifest.json')       , emit: generated_run_manifest
-    tuple val(meta), path('output/Metrics.csv')            , emit: metrics
-    tuple val(meta), path('output/UnassignedSequences.csv'), emit: unassigned
-    path "versions.yml"                             , emit: versions
+    tuple val(meta), path("output/Samples/*/*_R*.fastq.gz")    , emit: sample_fastq
+    tuple val(meta), path("output/Samples/*/*.json")           , emit: sample_json
+    tuple val(meta), path("output/info/*.log")                 , emit: b2f_log
+    tuple val(meta), path("output/*.html")                     , emit: qc_html
+    tuple val(meta), path("output/Metrics.csv")                , emit: metrics
+    tuple val(meta), path("output/RunManifest.csv")            , emit: run_manifest_csv
+    tuple val(meta), path("output/RunManifest.json")           , emit: run_manifest_json
+    tuple val(meta), path("output/RunParameters.json")         , emit: run_parameter_json
+    tuple val(meta), path("output/RunStats.json")              , emit: run_stats
+    tuple val(meta), path("output/UnassignedSequences.csv")    , emit: unassigned
+    tuple val(meta), path("output/info/RunManifestErrors.json"), optional: true, emit: manifest_errors_json
+    tuple val(meta), path("output/info/*.log")                 , emit: log
+    path "versions.yml"                                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,8 +33,6 @@
     def prefix = task.ext.prefix ?: "${meta.id}"
     def runManifest = run_manifest ? "-r ${run_manifest}" : ""
     """
-    ls
-
     bases2fastq \\
         -p $task.cpus \\
         $runManifest \\

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