diff --git a/CHANGELOG.md b/CHANGELOG.md
index fc243f3..7bcc2ce 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#99](https://github.com/nf-core/seqinspector/pull/99) Fix group reports for paired reads
 - [#107](https://github.com/nf-core/seqinspector/pull/107) Put SeqFU-stats section reports together
 - [#112](https://github.com/nf-core/seqinspector/pull/112) Making fastq_screen_references value to use parentDir
+- [#120](https://github.com/nf-core/seqinspector/pull/120) Run FastqScreen with subsampled data if available
 
 ### `Dependencies`
 
diff --git a/tests/NovaSeq6000.main_subsample.nf.test.snap b/tests/NovaSeq6000.main_subsample.nf.test.snap
index 3ba5046..05a8868 100644
--- a/tests/NovaSeq6000.main_subsample.nf.test.snap
+++ b/tests/NovaSeq6000.main_subsample.nf.test.snap
@@ -4,28 +4,28 @@
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aba942d1e6996b579f19798e5673f514",
             "multiqc_general_stats.txt:md5,ad1ec9c64cbdb1131a26aeb6de51e31c",
-            "multiqc_fastq_screen.txt:md5,2ff2485b1f197cb6228dd4350d1bd638",
+            "multiqc_fastq_screen.txt:md5,ede47a68cfe19144331104f4e51b6ee7",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,aa1b8d6adae86005ea7a8b2e901099b8",
             "multiqc_general_stats.txt:md5,c73c8d10568a56f6534d280fff701e60",
-            "multiqc_fastq_screen.txt:md5,c54d863ed3e68ee8bcb51c9ad85de9bc",
+            "multiqc_fastq_screen.txt:md5,025c2db89ab18864c2828f3f4e368d4f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ff996e1d3dc4a46e0c9535e54d51ccab",
             "multiqc_general_stats.txt:md5,834e1868b887171cfda72029bbbe2d3f",
-            "multiqc_fastq_screen.txt:md5,737dc47e74e5b2f2c590652788831eff",
+            "multiqc_fastq_screen.txt:md5,8028856af6d413fa3592900e16dbc99f",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,3df36ecfe76b25b0c22dcda84bce2b3b",
             "multiqc_general_stats.txt:md5,274a001b007521970f14d68bd176e5be",
-            "multiqc_fastq_screen.txt:md5,568f6b6d14562d01b5aaeb1a39e1cf3d",
+            "multiqc_fastq_screen.txt:md5,e3e01b13becd5e30c9c12e5313b795c7",
             "multiqc_citations.txt:md5,5f52d7a0141e4234c6069df9ef575c9a",
             "multiqc_fastqc.txt:md5,ce61b4ce4b1d76ec3f20de3bf0c9ec7f",
             "multiqc_general_stats.txt:md5,d476ad59458a035a329605d5284b6012",
-            "multiqc_fastq_screen.txt:md5,a4dca31413036d35899a35ba14b17ea5"
+            "multiqc_fastq_screen.txt:md5,61392eb28e735f293516bb81f463450a"
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2024-12-05T15:17:50.525033752"
+        "timestamp": "2025-10-07T13:46:20.210321"
     }
 }
\ No newline at end of file
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index 22d37c3..17b4702 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -72,7 +72,7 @@ workflow SEQINSPECTOR {
     //
     if (!("seqfu_stats" in skip_tools)) {
         SEQFU_STATS (
-            ch_samplesheet
+            ch_samplesheet // Not `ch_sample_sized` to get actual read count
             .map { meta, reads ->
                 [[id: "seqfu", sample_id: meta.id, tags: meta.tags], reads]
             }
@@ -99,7 +99,7 @@ workflow SEQINSPECTOR {
             .toList()
 
         FASTQSCREEN_FASTQSCREEN (
-            ch_samplesheet,
+            ch_sample_sized,
             ch_fastqscreen_refs
         )
         ch_multiqc_files = ch_multiqc_files.mix(FASTQSCREEN_FASTQSCREEN.out.txt)