|
22 | 22 | "@id": "./", |
23 | 23 | "@type": "Dataset", |
24 | 24 | "creativeWorkStatus": "InProgress", |
25 | | - "datePublished": "2026-04-28T11:21:19+00:00", |
26 | | - "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/codespaces/new/nf-core/proteinannotator)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.0.0)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[](https://nfcore.slack.com/channels/proteinannotator)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads ([`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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <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/running/run-pipelines#using-parameter-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, Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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", |
| 25 | + "datePublished": "2026-04-30T13:33:06+00:00", |
| 26 | + "description": "<h1>\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"docs/images/nf-core-proteinannotator_logo_dark.png\">\n <img alt=\"nf-core/proteinannotator\" src=\"docs/images/nf-core-proteinannotator_logo_light.png\">\n </picture>\n</h1>\n\n[](https://github.com/codespaces/new/nf-core/proteinannotator)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/4.0.2)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[](https://nfcore.slack.com/channels/proteinannotator)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that ...\n\n<!-- TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n-->\n\n<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the \"tube map\" design for that. See https://nf-co.re/docs/community/brand/workflow-schematics#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads ([`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/get_started/environment_setup/overview) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/get_started/run-your-first-pipeline) with `-profile test` before running the workflow on actual data.\n\n<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n-->\n\nNow, you can run the pipeline using:\n\n<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->\n\n```bash\nnextflow run nf-core/proteinannotator \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <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/running/run-pipelines#using-parameter-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, Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n<!-- TODO nf-core: If applicable, make list of people who have also contributed -->\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](docs/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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->\n<!-- If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->\n\n<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->\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", |
27 | 27 | "hasPart": [ |
28 | 28 | { |
29 | 29 | "@id": "main.nf" |
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99 | 99 | }, |
100 | 100 | "mentions": [ |
101 | 101 | { |
102 | | - "@id": "#768dc354-cb30-47a7-a783-860e546de7f6" |
| 102 | + "@id": "#98546a56-6e83-4ec1-afe3-9f475d1e5665" |
103 | 103 | } |
104 | 104 | ], |
105 | 105 | "name": "nf-core/proteinannotator" |
|
131 | 131 | } |
132 | 132 | ], |
133 | 133 | "dateCreated": "", |
134 | | - "dateModified": "2026-04-28T11:21:19Z", |
| 134 | + "dateModified": "2026-04-30T13:33:06Z", |
135 | 135 | "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", |
136 | 136 | "keywords": ["nf-core", "nextflow", "annotation", "proteomics"], |
137 | 137 | "license": ["MIT"], |
|
158 | 158 | "version": "!>=25.10.4" |
159 | 159 | }, |
160 | 160 | { |
161 | | - "@id": "#768dc354-cb30-47a7-a783-860e546de7f6", |
| 161 | + "@id": "#98546a56-6e83-4ec1-afe3-9f475d1e5665", |
162 | 162 | "@type": "TestSuite", |
163 | 163 | "instance": [ |
164 | 164 | { |
165 | | - "@id": "#d7864a2c-2e49-4382-b2d7-6ef302c393b8" |
| 165 | + "@id": "#1fd508d8-09e1-4bb0-b1e4-0e6c0b457402" |
166 | 166 | } |
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168 | 168 | "mainEntity": { |
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171 | 171 | "name": "Test suite for nf-core/proteinannotator" |
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173 | 173 | { |
174 | | - "@id": "#d7864a2c-2e49-4382-b2d7-6ef302c393b8", |
| 174 | + "@id": "#1fd508d8-09e1-4bb0-b1e4-0e6c0b457402", |
175 | 175 | "@type": "TestInstance", |
176 | 176 | "name": "GitHub Actions workflow for testing nf-core/proteinannotator", |
177 | 177 | "resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml", |
|
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