From 61e8bc76df53531049707dca86bb8fa13882551e Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Fri, 26 Jul 2024 11:38:08 +0200 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Daniel Lundin --- CHANGELOG.md | 2 +- conf/test_its_dada_taxonomy.config | 2 +- docs/output.md | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a40ff833..f888dc21 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Added` - [#765](https://github.com/nf-core/ampliseq/pull/765) - Added version R09-RS220 of curated GTDB 16S taxonomy: `sbdi-gtdb=R09-RS220-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy` -- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as options for `--sintax_ref_taxonomy` +- [#766](https://github.com/nf-core/ampliseq/pull/766) - Added version 10 of Unite as parameter for `--sintax_ref_taxonomy`: `unite-fungi=10.0` and `unite-alleuk=10.0` ### `Changed` diff --git a/conf/test_its_dada_taxonomy.config b/conf/test_its_dada_taxonomy.config index 60ef7a99..d704320b 100644 --- a/conf/test_its_dada_taxonomy.config +++ b/conf/test_its_dada_taxonomy.config @@ -12,7 +12,7 @@ params { config_profile_name = 'Test sintax profile' - config_profile_description = 'Minimal test dataset to check pipeline function when using sintax for taxonomy assignment' + config_profile_description = 'Minimal test dataset to check pipeline function for ITS data with the DADA2 taxonomy classifier' // Limit resources so that this can run on GitHub Actions max_cpus = 2 diff --git a/docs/output.md b/docs/output.md index 302af707..33278748 100644 --- a/docs/output.md +++ b/docs/output.md @@ -202,7 +202,7 @@ Optionally, ASV sequences can be filtered for rRNA sequences identified by Barrn #### Length filter -Optionally, a length filter can be used to reduce potential contamination after ASV computation. For example with 515f and 806r primers the majority of 16S rRNA amplicon sequences should have a length of 253 bp and amplicons that vary significantly are likely spurious. +Optionally, a length filter can be used to reduce potential contamination after ASV computation. For example with 515f and 806r primers the majority of 16S rRNA amplicon sequences should have a length of 253 bp and amplicons that differ significantly from this are likely spurious. The minimum ASV length threshold can be set by `--min_len_asv` and the maximum length threshold with `--max_len_asv`. If no threshold is set, the filter (and output) is omitted.