diff --git a/modules/nf-core/bases2fastq/main.nf b/modules/nf-core/bases2fastq/main.nf
index ef85af1ab0c..0edfa95c9c7 100644
--- a/modules/nf-core/bases2fastq/main.nf
+++ b/modules/nf-core/bases2fastq/main.nf
@@ -2,20 +2,20 @@ process BASES2FASTQ {
     tag "$meta.id"
     label 'process_high'
 
-    container "docker.io/elembio/bases2fastq:1.4.0"
+    container "docker.io/elembio/bases2fastq:1.8.0"
 
     input:
     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/**/*_stats.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
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/bases2fastq/tests/main.nf.test.snap b/modules/nf-core/bases2fastq/tests/main.nf.test.snap
index 31b44eb6273..a7eb1841f98 100644
--- a/modules/nf-core/bases2fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/bases2fastq/tests/main.nf.test.snap
@@ -58,7 +58,7 @@
                         "id": "sim-data",
                         "samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
                     },
-                    "Metrics.csv:md5,6275702afbe92d37db0c95c6097b91c3"
+                    "Metrics.csv:md5,1db1769b9b5917b8353e05bf8fd699c7"
                 ]
             ],
             [
@@ -67,7 +67,7 @@
                         "id": "sim-data",
                         "samplesheet": "/nf-core/test-datasets/demultiplex/testdata/sim-data/RunManifest.csv"
                     },
-                    "RunManifest.json:md5,5e9250f46525cda93499e1513fcd2846"
+                    "RunManifest.json:md5,d584cdf00f577937a6cb691bb5331fe8"
                 ]
             ],
             [
@@ -97,8 +97,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T12:54:06.924330844"
+        "timestamp": "2024-06-06T13:10:30.916899975"
     }
 }
\ No newline at end of file