From ac003b759478f093f37d6ec9a140270ef7e3ab6f Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Feb 2026 15:23:41 +0100 Subject: [PATCH] Bump versions --- .nf-core.yml | 2 +- CHANGELOG.md | 14 ++++++++++++++ assets/multiqc_config.yml | 2 +- nextflow.config | 2 +- ro-crate-metadata.json | 24 ++++++++++++------------ 5 files changed, 29 insertions(+), 15 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 64626f5..82938d0 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -15,4 +15,4 @@ template: skip_features: - fastqc - igenomes - version: 2.1.0 + version: 2.2.0dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 673ce3f..99fa09f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,20 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev - [unreleased] + +### `Added` + +### `Fixed` + +### `Dependencies` + +| Tool | Old Version | New Version | +| ---- | ----------- | ----------- | +| | | | + +### `Deprecated` + ## v2.1.0 - Gracious Goblin - [2026-02-10] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index e9b83f5..4138f9b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ report_comment: > - This report has been generated by the nf-core/createtaxdb analysis pipeline. For information about how to interpret these results, please see the documentation. + This report has been generated by the nf-core/createtaxdb analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-createtaxdb-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 4266d14..7d4ffa0 100644 --- a/nextflow.config +++ b/nextflow.config @@ -346,7 +346,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'main' nextflowVersion = '!>=25.04.2' - version = '2.1.0' + version = '2.2.0dev' doi = '10.5281/zenodo.15696114' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index fcdb78c..a935911 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2026-02-02T09:05:30+00:00", + "creativeWorkStatus": "InProgress", + "datePublished": "2026-02-10T14:22:41+00:00", "description": "

\n \n \n \"nf-core/createtaxdb\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/createtaxdb)\n[![GitHub Actions CI Status](https://github.com/nf-core/createtaxdb/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/createtaxdb/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/createtaxdb/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/createtaxdb/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/createtaxdb/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.15696114-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.15696114)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.4.1)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/createtaxdb)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23createtaxdb-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/createtaxdb)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/createtaxdb** is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input reference genome set in a highly automated and parallelised manner.\nIt supports both nucleotide and protein based classifiers and profilers.\nThe pipeline is designed to be a companion pipeline to [nf-core/taxprofiler](https://nf-co.re/taxprofiler/) for taxonomic profiling of metagenomic data, but can be used for any context.\n\n

\n \n \n \"nf-core/createtaxdb\"\n \n

\n\n1. Prepares input FASTA files for building\n2. Builds databases for:\n - [Bracken](https://doi.org/10.7717/peerj-cs.104)\n - [Centrifuge](https://doi.org/10.1101/gr.210641.116)\n - [DIAMOND](https://doi.org/10.1038/nmeth.3176)\n - [ganon](https://doi.org/10.1093/bioinformatics/btaa458)\n - [Kaiju](https://doi.org/10.1038/ncomms11257)\n - [KMCP](https://doi.org/10.1093/bioinformatics/btac845)\n - [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)\n - [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0)\n - [MALT](https://doi.org/10.1038/s41559-017-0446-6)\n - [sourmash](https://doi.org/10.21105/joss.06830)\n - [sylph](https://doi.org/10.1038/s41587-024-02412-y)\n - [MetaCache](https://doi.org/10.1093/bioinformatics/btx520)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare an input comma-separated table (csv) with your input reference genomes that looks as follows:\n\n| id | taxid | fasta_dna | fasta_aa |\n| ---------------------------------------- | ------ | ------------------------------------------- | ------------------------------------------- |\n| Human_Mitochondrial_genome | 9606 | chrMT.fna | |\n| SARS-CoV-2_genome | 694009 | GCA_011545545.1_ASM1154554v1_genomic.fna.gz | GCA_011545545.1_ASM1154554v1_genomic.faa.gz |\n| Bacteroides_fragilis_genome | 817 | GCF_016889925.1_ASM1688992v1_genomic.fna.gz | GCF_016889925.1_ASM1688992v1_genomic.faa.gz |\n| Candidatus_portiera_aleyrodidarum_genome | 91844 | GCF_000292685.1_ASM29268v1_genomic.fna | GCF_000292685.1_ASM29268v1_genomic.faa |\n| Haemophilus_influenzae_genome | 727 | GCF_900478275.1_34211_D02_genomic.fna | GCF_900478275.1_34211_D02_genomic.faa |\n| Streptococcus_agalactiae_genome | 1311 | | GCF_002881355.1_ASM288135v1_genomic.faa |\n\nEach row contains a human readable name, the taxonomic ID of the organism, and then an (optionally gzipped) Nucleotide and/or Amino Acid FASTA file.\n\nNow, with an appropriate set of taxonomy files you can build databases for multiple profilers - such as Kraken2, ganon, and DIAMOND - in parallel:\n\n```bash\nnextflow run nf-core/createtaxdb \\\n -profile \\\n --input samplesheet.csv \\\n --accession2taxid ///taxonomy/nucl_gb.accession2taxid \\\n --nucl2taxid ///taxonomy/nucl.accession2taxid.gz \\\n --prot2taxid ///taxonomy/prot.accession2taxid.gz \\\n --nodesdmp ///taxonomy/nodes.dmp \\\n --namesdmp ///taxonomy/names.dmp \\\n --build_kraken2 \\\n --kraken2_build_options='--kmer-len 45' \\\n --build_ganon \\\n --ganon_build_options='--kmer-size 45' \\\n --build_diamond \\\n --diamond_build_options='--no-parse-seqids' \\\n --build_metacache \\\n --outdir \n```\n\nThe output directory will contain directories containing the database files for each of the profilers you selected to build.\n\nYou can also generate pre-prepared input sheets for database specifications of pipelines such as [nf-core/taxprofiler](https://nf-co.re/taxprofiler) using `--generate_downstream_samplesheets`.\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/createtaxdb/usage) and the [parameter documentation](https://nf-co.re/createtaxdb/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/createtaxdb/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/createtaxdb/output).\n\n## Credits\n\nnf-core/createtaxdb was originally written by James A. Fellows Yates, Sam Wilkinson, Alexander Ramos D\u00edaz, Lili Andersson-Li and the nf-core community.\n\nIt has been extended by Moritz Beber (@Midnighter; adding sourmash support).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Zandra Fagern\u00e4s (@ZandraFagernas) for logo design\n- Paul Cantalupo (@pcantalupo) for additional documentation\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#createtaxdb` channel](https://nfcore.slack.com/channels/createtaxdb) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/createtaxdb for your analysis, please cite it using the following doi: [10.5281/zenodo.15696114](https://doi.org/10.5281/zenodo.15696114)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { @@ -102,7 +102,7 @@ }, "mentions": [ { - "@id": "#4d5ff26f-adab-4b50-a104-c915a3336e44" + "@id": "#7f78e30f-c824-4dc6-9d28-6c03d2f0cf44" } ], "name": "nf-core/createtaxdb" @@ -134,14 +134,14 @@ "@id": "#jfy133@gmail.com" }, { - "@id": "#jfy133@gmail.com" + "@id": "#sam1.wilkinson1@gmail.com" }, { - "@id": "#sam1.wilkinson1@gmail.com" + "@id": "#jfy133@gmail.com" } ], "dateCreated": "", - "dateModified": "2026-02-02T10:05:30Z", + "dateModified": "2026-02-10T15:22:41Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -172,10 +172,10 @@ }, "url": [ "https://github.com/nf-core/createtaxdb", - "https://nf-co.re/createtaxdb/2.1.0/" + "https://nf-co.re/createtaxdb/dev/" ], "version": [ - "2.1.0" + "2.2.0dev" ] }, { @@ -191,11 +191,11 @@ "version": "!>=25.04.2" }, { - "@id": "#4d5ff26f-adab-4b50-a104-c915a3336e44", + "@id": "#7f78e30f-c824-4dc6-9d28-6c03d2f0cf44", "@type": "TestSuite", "instance": [ { - "@id": "#4ff99c7d-a35f-439c-a8ae-3bfe5b82ca92" + "@id": "#880d272b-8cb7-4ac0-afa9-e2e8a68514b4" } ], "mainEntity": { @@ -204,7 +204,7 @@ "name": "Test suite for nf-core/createtaxdb" }, { - "@id": "#4ff99c7d-a35f-439c-a8ae-3bfe5b82ca92", + "@id": "#880d272b-8cb7-4ac0-afa9-e2e8a68514b4", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/createtaxdb", "resource": "repos/nf-core/createtaxdb/actions/workflows/nf-test.yml", @@ -341,7 +341,7 @@ "@id": "#jfy133@gmail.com", "@type": "Person", "email": "jfy133@gmail.com", - "name": "James Fellows Yates" + "name": "James A. Fellows Yates" }, { "@id": "#sam1.wilkinson1@gmail.com",