diff --git a/bin/taxref_reformat_qiime_greengenes2022.sh b/bin/taxref_reformat_qiime_greengenes2022.sh index aa4678a8..69c75fae 100755 --- a/bin/taxref_reformat_qiime_greengenes2022.sh +++ b/bin/taxref_reformat_qiime_greengenes2022.sh @@ -1,9 +1,5 @@ #!/bin/sh # Decompress files. -gzip -c -d 2022.10.seqs.fna.gz > 2022.10.seqs.fna -gzip -c -d 2022.10.taxonomy.md5.tsv.gz > 2022.10.taxonomy.md5.tsv - -# Select and rename files -mv *.fna greengenes2022.fna -mv *.tsv greengenes2022.tax +gzip -c -d *.seqs.fna.gz > greengenes2.fna +gzip -c -d *.taxonomy.md5.tsv.gz > greengenes2.tax diff --git a/conf/ref_databases.config b/conf/ref_databases.config index 157e835e..e89df338 100644 --- a/conf/ref_databases.config +++ b/conf/ref_databases.config @@ -330,7 +330,13 @@ params { citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139" fmtscript = "taxref_reformat_qiime_greengenes85.sh" } - 'greengenes2022' { + 'greengenes2' { + title = "Greengenes2 16S - Version 2022.10" + file = [ "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.seqs.fna.gz", "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.taxonomy.md5.tsv.gz" ] + citation = "McDonald, D., Jiang, Y., Balaban, M. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01845-1" + fmtscript = "taxref_reformat_qiime_greengenes2022.sh" + } + 'greengenes2=2022.10' { title = "Greengenes2 16S - Version 2022.10" file = [ "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.seqs.fna.gz", "http://ftp.microbio.me/greengenes_release/2022.10/2022.10.taxonomy.md5.tsv.gz" ] citation = "McDonald, D., Jiang, Y., Balaban, M. et al. Greengenes2 unifies microbial data in a single reference tree. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01845-1" diff --git a/nextflow_schema.json b/nextflow_schema.json index 0f00790f..29aee21e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -443,7 +443,8 @@ "unite-alleuk=8.2", "unite-alleuk", "greengenes85", - "greengenes2022" + "greengenes2", + "greengenes2=2022.10" ] }, "qiime_ref_tax_custom": {