diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
index d42be2cbd053..014896b04de2 100644
--- a/modules/nf-core/bases2fastq/main.nf
+++ b/modules/nf-core/bases2fastq/main.nf
@@ -8,15 +8,15 @@ process BASES2FASTQ {
     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/**/*_stats.json') , emit: sample_json
-    tuple val(meta), path('output/*_QC.html')               , emit: qc_report
-    tuple val(meta), path('output/multiqc_report.html')     , emit: multiqc_report, optional: true
-    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('*/Samples/**/*_R*.fastq.gz'), emit: sample_fastq
+    tuple val(meta), path('*/Samples/**/*_stats.json') , emit: sample_json
+    tuple val(meta), path('*/*_QC.html')               , emit: qc_report
+    tuple val(meta), path('*/multiqc_report.html')     , emit: multiqc_report, optional: true
+    tuple val(meta), path('*/RunStats.json')           , emit: run_stats
+    tuple val(meta), path('*/RunManifest.json')        , emit: generated_run_manifest
+    tuple val(meta), path('*/Metrics.csv')             , emit: metrics
+    tuple val(meta), path('*/UnassignedSequences.csv') , emit: unassigned
+    path "versions.yml"                                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,13 +28,15 @@ process BASES2FASTQ {
     }
     def args = task.ext.args ?: ''
     def runManifest = run_manifest ? "-r ${run_manifest}" : ""
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
     bases2fastq \\
         -p $task.cpus \\
         $runManifest \\
         $args \\
         $run_dir \\
-        output
+        $prefix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":