From bca3e47bdf43f5c4703569354a924fe550bfef7f Mon Sep 17 00:00:00 2001
From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com>
Date: Mon, 1 Jul 2024 14:54:02 +0000
Subject: [PATCH] Cutadapt: fix --par_quality_cutoff_r2

---
 CHANGELOG.md           | 5 ++++-
 src/cutadapt/script.sh | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9923a1d5..b5c403af 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@
 
 * `pear`: fix component not exiting with the correct exitcode when PEAR fails.
 
+* `cutadapt`: fix `--par_quality_cutoff_r2` argument.
+
+* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
+
 # biobox 0.1.0
 
 ## BREAKING CHANGES
@@ -12,7 +16,6 @@
   Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
   splitting up certain file paths.
 
-* `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
 
 ## NEW FEATURES
 
diff --git a/src/cutadapt/script.sh b/src/cutadapt/script.sh
index a1ea69f1..20c92724 100644
--- a/src/cutadapt/script.sh
+++ b/src/cutadapt/script.sh
@@ -127,7 +127,7 @@ mod_args=$(echo \
   ${par_cut_r2:+--cut_r2 "${par_cut_r2}"} \
   ${par_nextseq_trim:+--nextseq-trim "${par_nextseq_trim}"} \
   ${par_quality_cutoff:+--quality-cutoff "${par_quality_cutoff}"} \
-  ${par_quality_cutoff_r2:+--quality-cutoff_r2 "${par_quality_cutoff_r2}"} \
+  ${par_quality_cutoff_r2:+-Q "${par_quality_cutoff_r2}"} \
   ${par_quality_base:+--quality-base "${par_quality_base}"} \
   ${par_poly_a:+--poly-a} \
   ${par_length:+--length "${par_length}"} \