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Fix docker container permissions for ms2rescore #302

Merged
merged 7 commits into from
Feb 19, 2024
Merged

Fix docker container permissions for ms2rescore #302

merged 7 commits into from
Feb 19, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Jan 23, 2024 •
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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/mhcquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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 Jan 23, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f34ebc7

+| ✅ 200 tests passed       |+
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 53]

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-16 13:43:48

marissaDubbelaar
marissaDubbelaar reviewed Jan 23, 2024
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conf/modules.config Outdated
@@ -157,6 +157,7 @@ process {
}

withName: 'MS2RESCORE' {
containerOptions = '-u $(id -u) -e "HOME=${HOME}" -v $HOME:$HOME'
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Does this work like this or does it need to be process.containerOptions?

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process.containerOptions works only in the nextflow.config

I oriented myself by Julia's fix: nf-core/tools#2673

By this we can define container options on module level, that is not possible with runOptions

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And: The MS2Rescore container needed a specific "treatment" in order to run, else permission issues. Previously that was handled by userEmulation, but that is/will be removed :/

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Ok so this works when having sudo rights, but apparently not via GH actions.. Im gonna test the full diff compared to userEmulation

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To fix lints we need to wait for the newest template update. Conversation: https://nfcore.slack.com/archives/CE6PELWR4/p1705931019545439?thread_ts=1705482353.145949&cid=CE6PELWR4

marissaDubbelaar
marissaDubbelaar approved these changes Feb 19, 2024
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👍

@jonasscheid jonasscheid merged commit b9b2f2a into nf-core:dev Feb 19, 2024
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@jonasscheid jonasscheid mentioned this pull request Mar 4, 2024
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@jonasscheid jonasscheid mentioned this pull request Apr 25, 2024
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@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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@jonasscheid @marissaDubbelaar