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muffato merged 2 commits into from
Feb 2, 2026
Merged

Important! Template update for nf-core/tools v3.5.2 #44

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a8c5a6f
Template update for nf-core/tools version 3.5.2
sanger-tolsoft Feb 2, 2026
cb4dbb2
Merge branch 'dev' into nf-core-template-merge-3.5.2
muffato Feb 2, 2026
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2 changes: 1 addition & 1 deletion .nf-core.yml
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- manifest.homePage
- config_defaults:
- params.selected_fw_output
nf_core_version: 3.5.1
nf_core_version: 3.5.2
repository_type: pipeline
template:
author: "@muffato"
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4 changes: 2 additions & 2 deletions README.md
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[![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%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![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)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](https://docs.conda.io/en/latest/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![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/sanger-tol/sequencecomposition)
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6 changes: 3 additions & 3 deletions ro-crate-metadata.json
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"@id": "./",
"@type": "Dataset",
"creativeWorkStatus": "InProgress",
"datePublished": "2025-12-02T10:45:29+00:00",
"description": "# ![sanger-tol/sequencecomposition](docs/images/sanger-tol-sequencecomposition_logo.png)\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/sanger-tol/sequencecomposition)\n[![GitHub Actions CI Status](https://github.com/sanger-tol/sequencecomposition/actions/workflows/nf-test.yml/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/sanger-tol/sequencecomposition/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions/workflows/linting.yml)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14358108-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14358108)\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%A525.04.0-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=conda)](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/sanger-tol/sequencecomposition)\n\n## Introduction\n\n**sanger-tol/sequencecomposition** is a bioinformatics analysis pipeline that extracts statistics from a genome about its sequence composition.\n\nThe pipeline takes an assembly Fasta file (possibly compressed), runs `fasta_windows` on it, and transforms the outputs into files more practical for downstream use.\n\nSteps involved:\n\n- Run `fasta_windows` on the assembly Fasta file.\n- Extract single-statistics bedGraph files from the multi-statistics TSV\n files `fasta_windows` outputs.\n- Compress and index all bedGraph and TSV files with `bgzip` and `tabix`.\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\nThe easiest is to provide the path of the Fasta file to analyse like this:\n\n```console\nnextflow run sanger-tol/sequencecomposition --fasta /path/to/genome.fa\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\nThe pipeline also supports bulk downloads through a sample-sheet.\nMore information about this mode on our [pipeline website](https://pipelines.tol.sanger.ac.uk/sequencecomposition/usage).\n\n## Credits\n\nsanger-tol/sequencecomposition was originally written by [Matthieu Muffato](https://github.com/muffato).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews.\n- [Tyler Chafin](https://github.com/tkchafin) for updates.\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 `#pipelines` channel](https://sangertreeoflife.slack.com/channels/pipelines). Please [create an issue](https://github.com/sanger-tol/sequencecomposition/issues/new/choose) on GitHub if you are not on the Sanger slack channel.\n\n## Citations\n\nIf you use sanger-tol/sequencecomposition for your analysis, please cite it using the following doi: [10.5281/zenodo.14358108](https://doi.org/10.5281/zenodo.14358108)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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",
"datePublished": "2026-02-02T13:45:30+00:00",
"description": "# ![sanger-tol/sequencecomposition](docs/images/sanger-tol-sequencecomposition_logo.png)\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/sanger-tol/sequencecomposition)\n[![GitHub Actions CI Status](https://github.com/sanger-tol/sequencecomposition/actions/workflows/nf-test.yml/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/sanger-tol/sequencecomposition/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/sequencecomposition/actions/workflows/linting.yml)\n[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14358108-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14358108)\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%A525.04.0-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-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\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/sanger-tol/sequencecomposition)\n\n## Introduction\n\n**sanger-tol/sequencecomposition** is a bioinformatics analysis pipeline that extracts statistics from a genome about its sequence composition.\n\nThe pipeline takes an assembly Fasta file (possibly compressed), runs `fasta_windows` on it, and transforms the outputs into files more practical for downstream use.\n\nSteps involved:\n\n- Run `fasta_windows` on the assembly Fasta file.\n- Extract single-statistics bedGraph files from the multi-statistics TSV\n files `fasta_windows` outputs.\n- Compress and index all bedGraph and TSV files with `bgzip` and `tabix`.\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\nThe easiest is to provide the path of the Fasta file to analyse like this:\n\n```console\nnextflow run sanger-tol/sequencecomposition --fasta /path/to/genome.fa\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\nThe pipeline also supports bulk downloads through a sample-sheet.\nMore information about this mode on our [pipeline website](https://pipelines.tol.sanger.ac.uk/sequencecomposition/usage).\n\n## Credits\n\nsanger-tol/sequencecomposition was originally written by [Matthieu Muffato](https://github.com/muffato).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews.\n- [Tyler Chafin](https://github.com/tkchafin) for updates.\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 `#pipelines` channel](https://sangertreeoflife.slack.com/channels/pipelines). Please [create an issue](https://github.com/sanger-tol/sequencecomposition/issues/new/choose) on GitHub if you are not on the Sanger slack channel.\n\n## Citations\n\nIf you use sanger-tol/sequencecomposition for your analysis, please cite it using the following doi: [10.5281/zenodo.14358108](https://doi.org/10.5281/zenodo.14358108)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\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"
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}
],
"dateCreated": "",
"dateModified": "2025-12-02T10:45:29Z",
"dateModified": "2026-02-02T13:45:30Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nextflow",
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