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Ban references to Anaconda #119

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Ban references to Anaconda #119

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muffato
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@muffato muffato commented Oct 24, 2024 •
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@tkchafin: this is a draft PR to test stuff. Feel free to use it.

I've first removed all references to "defaults".
It's not clear if we should be making patches for all modules. nf-core modules patch does detect the difference and makes a patch (I've done it for samtools/flagstat) but nf-core lint and nf-core lint --release don't flag it up. I want to see what the CI says.

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
  • Make sure your code lints (nf-core 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).

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github-actions bot commented Oct 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ca9d582

+| ✅ 128 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2024-10-24 13:36:24

@gq1
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gq1 commented Oct 25, 2024

No module patch files, nf-core lint didn't complain? even if without any warnings.

These files are just static files and will not be used if we don't run in conda.

If we run in docker or singularity, it will still pull the prebuilt images remotely, default packages still included.

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muffato commented Nov 4, 2024

No module patch files, nf-core lint didn't complain? even if without any warnings.

Not that I could see. Not on CI either: https://github.com/sanger-tol/blobtoolkit/actions/runs/11500443253/job/32010690182?pr=119#step:6:423

These files are just static files and will not be used if we don't run in conda.

If we run in docker or singularity, it will still pull the prebuilt images remotely, default packages still included.

Absolutely, updating the environment.yml doesn't change anything for us in production, or for Sanger users who use our farm installation as a module. It's mostly an act of kindness for Conda users out there, incl. Sanger users who are not aware of our central install / singularity, so that they don't get caught in unnecessary Anaconda challenges.

@muffato
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muffato commented Nov 22, 2024

Closing in favour of #124

@muffato muffato closed this Nov 22, 2024
@muffato muffato deleted the anaconda_ban branch November 22, 2024 13:10
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