From d0e1ec8b5cd010f0f29f9b65cdea54551deed1ff Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 20 Dec 2024 16:51:36 +0100 Subject: [PATCH] Template update for nf-core/tools version 3.1.0 --- ro-crate-metadata.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 1e8a6e16..ed22547e 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,7 +22,7 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2024-12-20T15:50:33+00:00", + "datePublished": "2024-12-20T15:51:34+00:00", "description": "

\n \n \n \"nf-core/mag\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/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/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\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/mag)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23mag-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/mag)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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/mag** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))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/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\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/mag \\\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/mag/usage) and the [parameter documentation](https://nf-co.re/mag/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/mag/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/mag/output).\n\n## Credits\n\nnf-core/mag was originally written by Hadrien Gourl\u00e9, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\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 `#mag` channel](https://nfcore.slack.com/channels/mag) (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": "#363fcc6e-14d4-4e9f-a113-1bd2edc23cfd" + "@id": "#61fc8a70-8352-477b-91fe-e872b9c83a34" } ], "name": "nf-core/mag" @@ -132,7 +132,7 @@ } ], "dateCreated": "", - "dateModified": "2024-12-20T16:50:33Z", + "dateModified": "2024-12-20T16:51:34Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -184,11 +184,11 @@ "version": "!>=24.04.2" }, { - "@id": "#363fcc6e-14d4-4e9f-a113-1bd2edc23cfd", + "@id": "#61fc8a70-8352-477b-91fe-e872b9c83a34", "@type": "TestSuite", "instance": [ { - "@id": "#bc3a6403-7036-414f-b733-d08976d1d9c6" + "@id": "#9c4d8381-0b65-4e26-8495-b3e9cffdf75b" } ], "mainEntity": { @@ -197,7 +197,7 @@ "name": "Test suite for nf-core/mag" }, { - "@id": "#bc3a6403-7036-414f-b733-d08976d1d9c6", + "@id": "#9c4d8381-0b65-4e26-8495-b3e9cffdf75b", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/mag", "resource": "repos/nf-core/mag/actions/workflows/ci.yml",