From 88107cd27581a84c4658612b10199fad44762ebb Mon Sep 17 00:00:00 2001 From: vagkaratzas Date: Mon, 9 Feb 2026 14:53:17 +0000 Subject: [PATCH] zenodo updated --- README.md | 5 ++--- ro-crate-metadata.json | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fb552f8..2eef432 100644 --- a/README.md +++ b/README.md @@ -7,7 +7,7 @@ [![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) [![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) -[![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) +[![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.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![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/) @@ -99,8 +99,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 51bb9a3..8058a02 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2026-02-09T10:42:29+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 computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n

\n \n \n \"nf-core/proteinannotator\"\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 and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\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", + "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.18547735-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.18547735)\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 computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n

\n \n \n \"nf-core/proteinannotator\"\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 and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\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\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\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": [ { "@id": "main.nf"