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Refactor authors to list of contributors #222

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heuermh
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@heuermh heuermh commented Jan 17, 2025

Fixes #221

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/pangenome branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@heuermh heuermh mentioned this pull request Jan 17, 2025
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github-actions bot commented Jan 17, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0649f70

+| ✅ 213 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pangenome_logo_dark.png">\n <img alt="nf-core/pangenome" src="docs/images/nf-core-pangenome_logo_light.png">\n \n

    GitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\n\n## Introduction\n\nnf-core/pangenome 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 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 Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.Make sure to test your setup with -profile test before running the workflow on actual data.\n\n 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\nsamplesheet.csv:\n\ncsv\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 update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/pangenome \\\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.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/pangenome was originally written by Simon Heumos, Michael L Heuer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n 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.\n\nFor further information or help, don't hesitate to get in touch on the Slack #pangenome channel (you can join with this invite).\n\n## Citations\n\n 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/pangenome for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX 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 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.\n",
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_unchanged - Required pipeline config not found - {'manifest.author'}

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.1
  • Run at 2025-01-18 17:56:12

AndreaGuarracino
AndreaGuarracino reviewed Jan 17, 2025
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nextflow.config Outdated
],
[
name: 'Andrea Guarracino',
affiliation: """Genomics Research Centre, Human Technopole, Milan, Italy""",
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My affiliation is the same as Erik

University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA

AndreaGuarracino
AndreaGuarracino reviewed Jan 17, 2025
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nextflow.config Outdated
],
[
name: 'Erik Garrison',
affiliation: """The University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA""",
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Okay, but without the "The"

mirpedrol
mirpedrol reviewed Jan 18, 2025
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heuermh and others added 3 commits January 18, 2025 11:54
@heuermh heuermh requested a review from subwaystation January 23, 2025 18:01
Zethson
Zethson approved these changes Jan 27, 2025
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nextflow.config
email: '',
github: '@zethson',
contribution: ['contributor'],
orcid: ''
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https://orcid.org/0000-0002-8937-3457

FriederikeHanssen
FriederikeHanssen reviewed Jan 27, 2025
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README.md
| [Erik Garrison](https://github.com/ekg) | [The University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/) |
| [Andrea Guarracino](https://github.com/AndreaGuarracino) | [Genomics Research Centre, Human Technopole, Milan, Italy](https://humantechnopole.it/en/) <br> [The University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/) |
| [Erik Garrison](https://github.com/ekg) | [University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/) |
| [Andrea Guarracino](https://github.com/AndreaGuarracino) | [University of Tennessee Health Science Center, Memphis, Tennessee, TN, USA](https://uthsc.edu/) |
| [Friederike Hanssen](https://github.com/FriederikeHanssen) | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br> [Biomedical Data Science, Department of Computer Science, University of Tübingen, Germany](https://uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department/) |
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Suggested change
| [Friederike Hanssen](https://github.com/FriederikeHanssen) | [Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany](https://uni-tuebingen.de/en/research/research-infrastructure/quantitative-biology-center-qbic/) <br> [Biomedical Data Science, Department of Computer Science, University of Tübingen, Germany](https://uni-tuebingen.de/en/faculties/faculty-of-science/departments/computer-science/department/) |
| [Friederike Hanssen](https://github.com/FriederikeHanssen) | [Seqera](https://seqera/io) |

FriederikeHanssen
FriederikeHanssen reviewed Jan 27, 2025
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nextflow.config
email: '',
github: '@FriederikeHanssen',
contribution: ['contributor'],
orcid: ''
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Suggested change
orcid: ''
orcid: '[0009-0001-9875-5262](https://orcid.org/0009-0001-9875-5262)'

FriederikeHanssen
FriederikeHanssen reviewed Jan 27, 2025
View reviewed changes
nextflow.config
],
[
name: 'Friederike Hanssen',
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
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Suggested change
affiliation: """Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Germany""",
affiliation: """Seqera""",

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@AndreaGuarracino AndreaGuarracino AndreaGuarracino left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@mirpedrol mirpedrol mirpedrol left review comments

@Zethson Zethson Zethson approved these changes

@subwaystation subwaystation Awaiting requested review from subwaystation

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5 participants
@heuermh @mirpedrol @FriederikeHanssen @Zethson @AndreaGuarracino