8000 build: Set process arch for arm64 by edmundmiller · Pull Request #1888 · nf-core/sarek · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

build: Set process arch for arm64 #1888

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Draft
wants to merge 1 commit into
base: dev
Choose a base branch
from
Draft

build: Set process arch for arm64 #1888

wants to merge 1 commit into from
+1 −1

Conversation

edmundmiller
Copy link
Contributor
@edmundmiller edmundmiller commented May 6, 2025 •
edited
Loading

This should use arm64 based images on macos and linux.
For the nf-core arm profile we were use x86 emulation. This "translates" the instructions with rosetta under the hood.
Docker runs in a linux vm on Mac so it should be able to use the arm64
images natively.

nextflow run . -profile test,docker,arm,wave -resume --outdir results

Works as far as expected(we need to get the module dependencies updated)

@edmundmiller
build: Set process arch for arm64
36f12a5 
This should use arm64 based images on macos and linux.
For the nf-core arm profile we were use x86 emulation. This "translates" the instructions with rosetta under the hood.
Docker runs in a linux vm on Mac so it should be able to use the arm64
images natively.
@edmundmiller edmundmiller self-assigned this May 6, 2025
@nf-core-bot
Copy link
Member

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
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.

@github-actions GitHub Actions
Copy link
github-actions bot commented May 6, 2025

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36f12a5

+| ✅ 215 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-sarek_logo_dark.png">\n <img alt="nf-core/sarek" src="docs/images/nf-core-sarek_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/sarek 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/sarek \\\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/sarek was originally written by Maxime Garcia, Szilveszter Juhos, Friederike Hanssen.\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 #sarek 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/sarek 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",
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-05-06 13:38:43

@edmundmiller edmundmiller moved this to In Progress in nf-core co2 footprint May 6, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

At least 1 approving review is required to merge this pull request.

Assignees

@edmundmiller edmundmiller

Labels
None yet
Projects
arm64 software builds
Status: No status
nf-core co2 footprint
Status: In Progress
nf-core infrastructure projects
Status: In Progress
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@edmundmiller @nf-core-bot
0