Cutadapt: fix --par_quality_cutoff_r2

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
 

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}"} \