diff --git a/.nf-core.yml b/.nf-core.yml index 306897d..08bb8b9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -13,7 +13,7 @@ repository_type: pipeline template: author: Olga Botvinnik description: Generation of sequence-level annotations for amino acid sequences - version: 1.0.0dev + version: 1.0.0 force: true outdir: . skip_features: diff --git a/CHANGELOG.md b/CHANGELOG.md index c51aae7..e3d3d22 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.0.0dev - [date] +## v1.0.0 - [2026/02/04] Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template. @@ -17,15 +17,9 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https:// - [#60](https://github.com/nf-core/proteinannotator/pull/60) - Added nf-core module `S4PRED_RUNMODEL` for secondary structure prediction (i.e., α-helix, a β-strand or a coil). (by @vagkaratzas) - [#59](https://github.com/nf-core/proteinannotator/pull/59) - Added nf-core qc and pre-processing subworkflow for amino acid sequences `FAA_SEQFU_SEQKIT`. (by @vagkaratzas) - [#57](https://github.com/nf-core/proteinannotator/pull/57) - nf-core tools template update to 3.5.1. (by @vagkaratzas) -- [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing -- [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1 -- [#47](https://github.com/nf-core/proteinannotator/pull/47) - Update metromap with more tools added from [May 2025 Hackathon](https://nf-co.re/events/2025/hackathon-boston) -- [#42](https://github.com/nf-core/proteinannotator/pull/42) - Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md` -- [#13](https://github.com/nf-core/proteinannotator/pull/13) - Add nf-core seqkit/stats module -- [#9](https://github.com/nf-core/proteinannotator/pull/9) - Added [InterProScan](https://interproscan-docs.readthedocs.io/) module - local version - -### `Fixed` - -### `Dependencies` - -### `Deprecated` +- [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing. (by @edmundmiller, @olgabot) +- [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1. (by @olgabot) +- [#47](https://github.com/nf-core/proteinannotator/pull/47) - Update metromap with more tools added from [May 2025 Hackathon](https://nf-co.re/events/2025/hackathon-boston). (by @olgabot) +- [#42](https://github.com/nf-core/proteinannotator/pull/42) - Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`. (by @olgabot) +- [#13](https://github.com/nf-core/proteinannotator/pull/13) - Add nf-core seqkit/stats module. (by @olgabot, @heuermh) +- [#9](https://github.com/nf-core/proteinannotator/pull/9) - Added [InterProScan](https://interproscan-docs.readthedocs.io/) module - local version. (by @olgabot, @heuermh, @eweizy) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index bf478c5..e9ddc17 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,5 @@ report_comment: > - This report has been generated by the nf-core/proteinannotator - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/proteinannotator analysis pipeline. For information about how to interpret these results, please see the documentation. report_section_order: "nf-core-proteinannotator-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index ef821b5..e56f91f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -199,8 +199,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa // Load nf-core/proteinannotator custom profiles from different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinannotator.config" : "/dev/null" +includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/proteinannotator.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled @@ -287,7 +286,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=25.10.0' - version = '1.0.0dev' + version = '1.0.0' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 7dc9eef..08e223e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,8 +21,8 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "InProgress", - "datePublished": "2026-01-29T12:38:19+00:00", + "creativeWorkStatus": "Stable", + "datePublished": "2026-02-04T13:01:04+00:00", "description": "

\n \n \n \"nf-core/proteinannotator\"\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/proteinannotator)\n[![GitHub Actions CI Status](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinannotator/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/proteinannotator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\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%A525.10.0-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/3.5.1)\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/proteinannotator)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23proteinannotator-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/proteinannotator)[![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/proteinannotator** is a bioinformatics pipeline that runs statistics of input protein fasta files and identifies\nprotein annotations such as conserved domains, functions and secondary structure features, based on their sequence data.\n\n

\n \n \n \"Protein\n \n

\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)\n2. Functional annotation:\n - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`MultiQC`](http://multiqc.info/))\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 a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a fasta file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/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/proteinannotator/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/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Evangelos Karatzas](https://github.com/vagkaratzas)\n- [Martin Beracochea](https://github.com/mberacochea)\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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\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": [ { @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#197892e0-6893-41d7-acaa-49c7432f2b49" + "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2" } ], "name": "nf-core/proteinannotator" @@ -132,7 +132,7 @@ } ], "dateCreated": "", - "dateModified": "2026-01-29T12:38:19Z", + "dateModified": "2026-02-04T13:01:04Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -157,10 +157,10 @@ }, "url": [ "https://github.com/nf-core/proteinannotator", - "https://nf-co.re/proteinannotator/dev/" + "https://nf-co.re/proteinannotator/1.0.0/" ], "version": [ - "1.0.0dev" + "1.0.0" ] }, { @@ -176,11 +176,11 @@ "version": "!>=25.10.0" }, { - "@id": "#197892e0-6893-41d7-acaa-49c7432f2b49", + "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2", "@type": "TestSuite", "instance": [ { - "@id": "#2a8f2a5c-09bf-45df-81da-ccf721407355" + "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b" } ], "mainEntity": { @@ -189,7 +189,7 @@ "name": "Test suite for nf-core/proteinannotator" }, { - "@id": "#2a8f2a5c-09bf-45df-81da-ccf721407355", + "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/proteinannotator", "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml", diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 76cd534..ac75f97 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -43,7 +43,7 @@ "untar": 1.34 }, "Workflow": { - "nf-core/proteinannotator": "v1.0.0dev" + "nf-core/proteinannotator": "v1.0.0" } }, [ @@ -222,6 +222,6 @@ "nf-test": "0.9.3", "nextflow": "25.10.3" }, - "timestamp": "2026-02-04T10:35:30.572658533" + "timestamp": "2026-02-04T12:43:32.273407057" } } \ No newline at end of file