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enable conda #120

Merged
merged 2 commits into from
May 8, 2024
Merged

enable conda #120

merged 2 commits into from
May 8, 2024

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tillenglert
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I tested -profile conda using the test_assembly_only test which should use most of the modules. Still some adjustments needed to be done to actually run the pipeline using conda.

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/metapep branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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 May 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8453941

+| ✅ 177 tests passed       |+
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-03 07:53:03

skrakau
skrakau reviewed May 3, 2024
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nextflow.config
@@ -110,7 +110,7 @@ profiles {
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
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@skrakau skrakau May 3, 2024 •
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Why did this needed to be changed? It seemed at other locations it's still used as before?

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This seems to be a silent bug since dec 2022! I already posted this on slack: https://nfcore.slack.com/archives/CE5LG7WMB/p1714721754644179

Without the conda. it is not considered for the creation of the environment! This is probably also an issue in nf-core/epitopeprediction! @jonasscheid

skrakau
skrakau approved these changes May 8, 2024
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LGTM!

@tillenglert tillenglert merged commit 936ebbc into nf-core:dev May 8, 2024
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@tillenglert tillenglert deleted the enable-conda branch May 8, 2024 10:17
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@skrakau skrakau skrakau approved these changes

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@tillenglert @skrakau