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}"} \