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Upgrade Comet to latest 20223010 version #88

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merged 1 commit into from
Mar 24, 2023
Merged

Upgrade Comet to latest 20223010 version #88

merged 1 commit into from
Mar 24, 2023

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ypriverol
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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/quantms 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).

@ypriverol ypriverol linked an issue Mar 22, 2023 that may be closed by this pull request
Upgrade to OpenMS 1.9.1 with Comet 2023 #87
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@ypriverol ypriverol requested a review from jpfeuffer March 22, 2023 08:34
@ypriverol ypriverol changed the title upgrade the singularity and docker images Upgrade Comet to latest 20223010 version Mar 22, 2023
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github-actions bot commented Mar 22, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit f0c0a53

+| ✅ 155 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-22 08:35:23

@jpfeuffer
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Probably a conda parallelism error

@ypriverol
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Probably a conda parallelism error

Since two days ago, conda and mamba needs to be retried multiple times. 😜

@jpfeuffer
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One needs to use micromamba.
https://github.com/nf-core/quantms/blob/master/.github/workflows/ci.yml#L63

Python based conda and mamba are bugged when it gets to parallel access to the environments

@ypriverol ypriverol merged commit d29bd03 into nf-core:dev Mar 24, 2023
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@fabianegli fabianegli fabianegli approved these changes

@jpfeuffer jpfeuffer Awaiting requested review from jpfeuffer

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Upgrade to OpenMS 1.9.1 with Comet 2023
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@ypriverol @jpfeuffer @fabianegli