Template update for nf-core/tools version 3.1.1 #532
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fellen31
changed the title
jemten
reviewed
Jan 17, 2025
| @@ -12,6 +11,7 @@ lint: | |||
| - .github/workflows/awsfulltest.yml | |||
| - conf/modules.config | |||
| - conf/igenomes_ignored.config | |||
| - conf/test_full.config | |||
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This file is removed in the PR. Does it need to be here then?
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Yes, since we don't have a full test I removed the file, then it's needs to be in this list so the linting doesn't fail.
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| affiliation: '', | ||
| email: '', | ||
| github: '', | ||
| contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') | ||
| orcid: '' |
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Should we update this ina later PR?
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Sounds good, will gather up and fix in #534
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| beforeText = """ | ||
| \033[0;34m _ _ _ _ | ||
| \033[0;34m __ _ ___ _ __ ___ _ __ ___ (_) ___ _ __ ___ ___ __| (_) ___(_)_ __ ___ | ||
| \033[0;34m / _` |/ _ \\ '_ \\ / _ \\| '_ ` _ \\| |/ __|____| '_ ` _ \\ / _ \\/ _` | |/ __| | '_ \\ / _ \\_____ | ||
| \033[0;34m | (_| | __/ | | | (_) | | | | | | | (_|_____| | | | | | __/ (_| | | (__| | | | | __/_____| | ||
| \033[0;34m \\__, |\\___|_| |_|\\___/|_| |_| |_|_|\\___| |_| |_| |_|\\___|\\__,_|_|\\___|_|_| |_|\\___| | ||
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| \033[0;34m / __\\ \\ /\\ / / _ \\/ _` |/ _ \\ '_ \\ / / '_ \\ / _` | | |/ _ \\ | ||
| \033[0;34m \\__ \\\\ V V / __/ (_| | __/ | | |/ /| | | | (_| | | | (_) | | ||
| \033[0;34m |___/ \\_/\\_/ \\___|\\__,_|\\___|_| |_/_/ |_| |_|\\__,_|_|_|\\___/ | ||
| \033[0;34m | ||
| """ |
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No nallo logo on launch anymore 😢
ramprasadn
reviewed
Jan 17, 2025
ro-crate-metadata.json
Outdated
| "@type": "Dataset", | ||
| "creativeWorkStatus": "InProgress", | ||
| "datePublished": "2025-01-16T12:58:29+00:00", | ||
| "description": "# genomic-medicine-sweden/nallo\n\n[](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml)\n[](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\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/genomic-medicine-sweden/nallo)\n\n## Introduction\n\n**genomic-medicine-sweden/nallo** 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/contributing/design_guidelines#examples for examples. -->\n<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. 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<!-- 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 genomic-medicine-sweden/nallo \\\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/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\ngenomic-medicine-sweden/nallo was originally written by Felix Lenner.\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](.github/CONTRIBUTING.md).\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 genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- 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\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", |
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Don't forget to update the TODOs here 😄
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Thanks, missed this file. Not 100% sure how it should look like, but I updated the description and removed nf-core references.
jemten
approved these changes
Jan 17, 2025
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).