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Merged
merged 1 commit into from
May 24, 2025
Merged

Added CUDA test for runsOn #534

merged 1 commit into from
May 24, 2025

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GallVp
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@GallVp GallVp commented May 24, 2025

PR checklist

Closes #531

  • Added CUDA test for runsOn which is already configured.
  • 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/methylseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@GallVp GallVp requested a review from a team as a code owner May 24, 2025 08:41
@GallVp GallVp requested a review from FelixKrueger May 24, 2025 08:41
@GallVp GallVp linked an issue May 24, 2025 that may be closed by this pull request
GPU test on singularity fails #532
Closed
@GallVp GallVp requested a review from sateeshperi May 24, 2025 08:42
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented May 24, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 93c1ed0

+| ✅ 202 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

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

    \n\nGitHub 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/methylseq 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/methylseq \\\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/methylseq was originally written by Phil Ewels, Sateesh Peri.\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 #methylseq 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/methylseq for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n 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",

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-05-24 08:42:40

@GallVp
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GallVp commented May 24, 2025

Hi @sateeshperi

Looks like removing the GPU runner from the Get Shared step fixes the GPU problem. This is also suggested by the PR by @mashehu: #524

@GallVp GallVp mentioned this pull request May 24, 2025
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@GallVp GallVp merged commit 5fbed9c into dev May 24, 2025
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@GallVp GallVp deleted the use/runs_on branch May 24, 2025 16:44
@GallVp GallVp linked an issue May 26, 2025 that may be closed by this pull request
switch CI to runson #531
Closed
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@sateeshperi sateeshperi sateeshperi approved these changes

@FelixKrueger FelixKrueger Awaiting requested review from FelixKrueger FelixKrueger is a code owner automatically assigned from nf-core/methylseq

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GPU test on singularity fails switch CI to runson
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