From b98f1b77d1f6585995f00fb9189ad40c279417bd Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Fri, 16 Sep 2022 14:34:52 +0200
Subject: [PATCH] Bump bcl-convert version (#2077)

* Update main.nf

* update test.yml

* prettier
---
 modules/bclconvert/main.nf        |  2 +-
 tests/modules/bclconvert/test.yml | 10 ++++++++--
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/modules/bclconvert/main.nf b/modules/bclconvert/main.nf
index c5fdaaf6..3793674a 100644
--- a/modules/bclconvert/main.nf
+++ b/modules/bclconvert/main.nf
@@ -5,7 +5,7 @@ process BCLCONVERT {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using bcl-convert. Please use docker or singularity containers."
     }
-    container "nfcore/bclconvert:3.10.5"
+    container "nfcore/bclconvert:4.0.3"
 
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
diff --git a/tests/modules/bclconvert/test.yml b/tests/modules/bclconvert/test.yml
index 74aab696..1ee3fac5 100644
--- a/tests/modules/bclconvert/test.yml
+++ b/tests/modules/bclconvert/test.yml
@@ -7,16 +7,22 @@
     - path: output/bclconvert/Logs/FastqComplete.txt
     - path: output/bclconvert/Logs/Info.log
     - path: output/bclconvert/Logs/Warnings.log
+    - path: output/bclconvert/Reports/Adapter_Cycle_Metrics.csv
+      md5sum: 5a0c88793b4a0885fe3dda16609b576e
     - path: output/bclconvert/Reports/Adapter_Metrics.csv
       md5sum: 989240b8840b2169ac1061f952c90f6c
     - path: output/bclconvert/Reports/Demultiplex_Stats.csv
       md5sum: 93949a8cd96f907d83e0808c1ec2a04b
+    - path: output/bclconvert/Reports/Demultiplex_Tile_Stats.csv
+      md5sum: 83120160b0f22a1303fa1db31c19f6e9
     - path: output/bclconvert/Reports/IndexMetricsOut.bin
       md5sum: 9e688c58a5487b8eaf69c9e1005ad0bf
     - path: output/bclconvert/Reports/Index_Hopping_Counts.csv
       md5sum: 1059369e375fd8f8423c0f6c934be978
     - path: output/bclconvert/Reports/Quality_Metrics.csv
       md5sum: 6614accb1bb414fe312b17b81f5521f7
+    - path: output/bclconvert/Reports/Quality_Tile_Metrics.csv
+      md5sum: cdc89fd2962bdd4a24f71e186112118a
     - path: output/bclconvert/Reports/RunInfo.xml
       md5sum: 03038959f4dd181c86bc97ae71fe270a
     - path: output/bclconvert/Reports/SampleSheet.csv
@@ -26,9 +32,9 @@
     - path: output/bclconvert/Reports/fastq_list.csv
       md5sum: 05bc84f51840f5754cfb8381b36f2cb0
     - path: output/bclconvert/Sample1_S1_L001_R1_001.fastq.gz
-      md5sum: 57d2f3b389656245f923351d3e3d2d65
+      md5sum: 0a0341e2990b4fa1d9ad4b4c603144c1
     - path: output/bclconvert/Undetermined_S0_L001_R1_001.fastq.gz
-      md5sum: a4745abc5e7fdb89cc6df3069f3c6e69
+      md5sum: febef808ae5397ea4ee7ee40e5fd39e0
     - path: output/bclconvert/flowcell/InterOp/ControlMetricsOut.bin
       md5sum: 6d77b38d0793a6e1ce1e85706e488953
     - path: output/bclconvert/flowcell/InterOp/CorrectedIntMetricsOut.bin