From 2c4dc67273d1b25f45fbaeaff9e44d1d106db032 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 23 Jul 2024 14:05:15 +0200 Subject: [PATCH 1/2] Add sbdi-gtdb R09-RS220 --- conf/ref_databases.config | 14 +++++++++++--- nextflow_schema.json | 7 ++++--- .../local/utils_nfcore_ampliseq_pipeline/main.nf | 12 +++++++++++- 3 files changed, 26 insertions(+), 7 deletions(-) diff --git a/conf/ref_databases.config b/conf/ref_databases.config index c2db0ed2..b33c903e 100644 --- a/conf/ref_databases.config +++ b/conf/ref_databases.config @@ -130,11 +130,19 @@ params { dbversion = "RDP 18/11.5 (https://zenodo.org/record/4310151/)" } 'sbdi-gtdb' { - title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R08-RS214-1" - file = [ "https://figshare.scilifelab.se/ndownloader/files/45818841", "https://figshare.scilifelab.se/ndownloader/files/45818850" ] + title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1" + file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ] citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6" fmtscript = "taxref_reformat_sbdi-gtdb.sh" - dbversion = "SBDI-GTDB-R08-RS214-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/6)" + dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)" + taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species" + } + 'sbdi-gtdb=R09-RS220-1' { + title = "SBDI-GTDB - Sativa curated 16S GTDB database - Release R09-RS220-1" + file = [ "https://figshare.scilifelab.se/ndownloader/files/47244061", "https://figshare.scilifelab.se/ndownloader/files/47244076" ] + citation = "Lundin D, Andersson A. SBDI Sativa curated 16S GTDB database. FigShare. doi: 10.17044/scilifelab.14869077.v6" + fmtscript = "taxref_reformat_sbdi-gtdb.sh" + dbversion = "SBDI-GTDB-R09-RS220-1 (https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/7)" taxlevels = "Domain,Kingdom,Phylum,Class,Order,Family,Genus,Species" } 'sbdi-gtdb=R08-RS214-1' { diff --git a/nextflow_schema.json b/nextflow_schema.json index ceaf9366..2b977c0a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -372,10 +372,11 @@ "rdp", "rdp=18", "sbdi-gtdb", - "sbdi-gtdb=R06-RS202-1", - "sbdi-gtdb=R06-RS202-3", - "sbdi-gtdb=R07-RS207-1", + "sbdi-gtdb=R09-RS220-1", "sbdi-gtdb=R08-RS214-1", + "sbdi-gtdb=R07-RS207-1", + "sbdi-gtdb=R06-RS202-3", + "sbdi-gtdb=R06-RS202-1", "silva", "silva=132", "silva=138", diff --git a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf index 321463ae..6a31f97f 100644 --- a/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_ampliseq_pipeline/main.nf @@ -237,7 +237,17 @@ def validateInputParameters() { error("Incompatible parameters: `--filter_ssu` cannot be used with `--skip_barrnap` because filtering for SSU's depends on barrnap.") } - String[] sbdi_compatible_databases = ["coidb","coidb=221216","gtdb","gtdb=R09-RS220","gtdb=R08-RS214","gtdb=R07-RS207","gtdb=R06-RS202","gtdb=R05-RS95","midori2-co1","midori2-co1=gb250","pr2","pr2=5.0.0","pr2=4.14.0","pr2=4.13.0","rdp","rdp=18","sbdi-gtdb","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1","silva","silva=138","silva=132","unite-fungi","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2","unite-alleuk","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2"] + String[] sbdi_compatible_databases = [ + "coidb","coidb=221216", + "gtdb","gtdb=R09-RS220","gtdb=R08-RS214","gtdb=R07-RS207","gtdb=R06-RS202","gtdb=R05-RS95", + "midori2-co1","midori2-co1=gb250", + "pr2","pr2=5.0.0","pr2=4.14.0","pr2=4.13.0", + "rdp","rdp=18", + "sbdi-gtdb","sbdi-gtdb=R09-RS220-1","sbdi-gtdb=R08-RS214-1","sbdi-gtdb=R07-RS207-1", + "silva","silva=138","silva=132", + "unite-fungi","unite-fungi=9.0","unite-fungi=8.3","unite-fungi=8.2", + "unite-alleuk","unite-alleuk=9.0","unite-alleuk=8.3","unite-alleuk=8.2" + ] if (params.sbdiexport){ if (params.sintax_ref_taxonomy ) { if (!Arrays.stream(sbdi_compatible_databases).anyMatch(entry -> params.sintax_ref_taxonomy.toString().equals(entry)) ) { From 0b9a70bb2adf08ca33a5c61b0925d120eeb5d762 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 23 Jul 2024 14:08:03 +0200 Subject: [PATCH 2/2] Updated CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5fcf89b5..60879ee4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,8 @@ 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` + ### `Changed` - [#762](https://github.com/nf-core/ampliseq/pull/762) - Improved output documentation section "Optional ASV filtering" and parameter documentation