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fix --dada_ref_taxonomy silva=132 #786

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Oct 25, 2024
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fix --dada_ref_taxonomy silva=132 #786

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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,13 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#786](https://github.com/nf-core/ampliseq/pull/786) - Added version 20240904 of Kraken2 standard taxonomy database: `standard=20240904` or `standard` as parameter to `--kraken2_ref_taxonomy`

### `Changed`

- [#785](https://github.com/nf-core/ampliseq/pull/785) - replaced https://data.ace.uq.edu.au/public/gtdb/data by https://data.gtdb.ecogenomic.org for GTDB versions via `--dada_ref_taxonomy`

### `Fixed`

- [#785](https://github.com/nf-core/ampliseq/pull/785) - Template update for nf-core/tools version 3.0.2
- [#786](https://github.com/nf-core/ampliseq/pull/786) - Creation of the summary report was failing with `--dada_ref_taxonomy silva=132`

### `Dependencies`

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13 changes: 10 additions & 3 deletions conf/ref_databases.config
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Expand Up @@ -192,7 +192,7 @@ params {
dbversion = "SILVA v138.1 (https://zenodo.org/record/4587955)"
}
'silva=132' {
title = "Silva Project's version 132 release"
title = "Silva Projects version 132 release"
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file = [ "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz", "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz" ]
citation = "Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28. PMID: 23193283; PMCID: PMC3531112."
fmtscript = "taxref_reformat_standard.sh"
Expand Down Expand Up @@ -528,8 +528,15 @@ params {
taxlevels = "D,P,C,O,F,G,S"
}
'standard' {
title = "Standard database - Version 20230605"
file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz" ]
title = "Standard database - Version 20240904"
file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz" ]
citation = "Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0"
fmtscript = ""
taxlevels = "D,P,C,O,F,G,S"
}
'standard=20240904' {
title = "Standard database - Version 20240904"
file = [ "https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20240904.tar.gz" ]
citation = "Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0"
fmtscript = ""
taxlevels = "D,P,C,O,F,G,S"
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1 change: 1 addition & 0 deletions nextflow_schema.json
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Expand Up @@ -479,6 +479,7 @@
"greengenes",
"greengenes=13.5",
"standard",
"standard=20240904",
"standard=20230605"
]
},
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