From f0bf4344fe375eec47d4c0cf915f1d5b7bf7b8f1 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Thu, 12 Feb 2026 06:55:10 +0100
Subject: [PATCH 1/2] Rename bclconvert stats dir

---
 main.nf                                                         | 2 +-
 .../Unaligned/{Reports => Stats}/Adapter_Metrics.csv            | 0
 .../Unaligned/{Reports => Stats}/Demultiplex_Stats.csv          | 0
 .../Unaligned/{Reports => Stats}/Quality_Metrics.csv            | 0
 .../Unaligned/{Reports => Stats}/RunInfo.xml                    | 0
 5 files changed, 1 insertion(+), 1 deletion(-)
 rename test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/{Reports => Stats}/Adapter_Metrics.csv (100%)
 rename test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/{Reports => Stats}/Demultiplex_Stats.csv (100%)
 rename test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/{Reports => Stats}/Quality_Metrics.csv (100%)
 rename test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/{Reports => Stats}/RunInfo.xml (100%)

diff --git a/main.nf b/main.nf
index 836f468..fd5d72f 100644
--- a/main.nf
+++ b/main.nf
@@ -130,7 +130,7 @@ workflow CHECK_RUN_QUALITY {
     main:
         if (params.demultiplexer == 'bclconvert') {
             Channel.fromPath([
-            "${params.run_folder}/${params.demultiplexer_outdir}/Reports/*.csv",
+            "${params.run_folder}/${params.demultiplexer_outdir}/Stats/*.csv",
             "${params.run_folder}/RunInfo.xml"])
             .collect().ifEmpty([])
             .set { demux_stats }
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Adapter_Metrics.csv b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Adapter_Metrics.csv
similarity index 100%
rename from test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Adapter_Metrics.csv
rename to test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Adapter_Metrics.csv
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Demultiplex_Stats.csv b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Demultiplex_Stats.csv
similarity index 100%
rename from test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Demultiplex_Stats.csv
rename to test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Demultiplex_Stats.csv
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Quality_Metrics.csv b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Quality_Metrics.csv
similarity index 100%
rename from test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/Quality_Metrics.csv
rename to test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/Quality_Metrics.csv
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/RunInfo.xml b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/RunInfo.xml
similarity index 100%
rename from test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Reports/RunInfo.xml
rename to test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/Stats/RunInfo.xml

From d682ef5cf2f247f23e76ac1cef6669fe48400928 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Thu, 12 Feb 2026 07:09:53 +0100
Subject: [PATCH 2/2] Add bclconvert to top modules

---
 config/tool_config/multiqc_flowcell_config.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/tool_config/multiqc_flowcell_config.yaml b/config/tool_config/multiqc_flowcell_config.yaml
index 3c6205e..5830aef 100644
--- a/config/tool_config/multiqc_flowcell_config.yaml
+++ b/config/tool_config/multiqc_flowcell_config.yaml
@@ -17,5 +17,6 @@ table_columns_visible:
 top_modules:
     - 'custom_content'
     - 'bcl2fastq'
+    - 'bclconvert'
     - 'interop'