Post Gracious Goblin version bump

.nf-core.yml

@@ -15,4 +15,4 @@ template:
   skip_features:
     - fastqc
     - igenomes
-  version: 2.1.0
+  version: 2.2.0dev

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`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/createtaxdb/releases/tag/2.1.0" target="_blank">nf-core/createtaxdb</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/createtaxdb/2.1.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/createtaxdb/tree/dev" target="_blank">nf-core/createtaxdb</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/createtaxdb/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-createtaxdb-methods-description":
     order: -1000

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'
 }
 

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": "<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-createtaxdb_logo_dark_tax.png\">\n    <img alt=\"nf-core/createtaxdb\" src=\"docs/images/nf-core-createtaxdb_logo_light_tax.png\">\n  </picture>\n</h1>\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<h1>\n  <picture>\n    <source media=\"(prefers-color-scheme: dark)\" srcset=\"assets/createtaxdb-metromap-diagram-dark.png\">\n    <img alt=\"nf-core/createtaxdb\" src=\"assets/createtaxdb-metromap-diagram-light.png\">\n  </picture>\n</h1>\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 <docker/singularity/.../institute> \\\n   --input samplesheet.csv \\\n   --accession2taxid /<path>/<to>/taxonomy/nucl_gb.accession2taxid \\\n   --nucl2taxid /<path>/<to>/taxonomy/nucl.accession2taxid.gz \\\n   --prot2taxid /<path>/<to>/taxonomy/prot.accession2taxid.gz \\\n   --nodesdmp /<path>/<to>/taxonomy/nodes.dmp \\\n   --namesdmp /<path>/<to>/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 <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",