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feat(wave): adding profile seqera_containers #1291

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maxulysse
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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/rnaseq 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>).
  • 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).

@maxulysse maxulysse mentioned this pull request Apr 30, 2024
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github-actions bot commented Apr 30, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c27b63f

+| ✅ 171 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-13 16:11:31

maxulysse
maxulysse commented Apr 30, 2024
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pditommaso
pditommaso reviewed May 12, 2024
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@@ -248,6 +248,13 @@ profiles {
shifter.enabled = false
charliecloud.enabled = false
}
wave {
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Wonder if this should be called seqera-container

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What about community-containers?

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Maybe you are right, though, because "Bio(containers)" is prefixed by the Bioconda community.

@drpatelh drpatelh added this to the 3.15.0 milestone May 13, 2024
drpatelh
drpatelh reviewed May 13, 2024
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@drpatelh @pditommaso
Apply suggestions from code review
a37afbf 
Co-authored-by: Paolo Di Tommaso <[email protected]>
maxulysse
maxulysse commented May 13, 2024
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@drpatelh @maxulysse
Update CHANGELOG.md
d7b0037 
Co-authored-by: Maxime U Garcia <[email protected]>
drpatelh
drpatelh reviewed May 13, 2024
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drpatelh
drpatelh reviewed May 13, 2024
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@drpatelh drpatelh mentioned this pull request May 13, 2024
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@drpatelh drpatelh changed the title feat(wave): adding profile wave feat(wave): adding profile seqera_containers May 13, 2024
ewels
ewels approved these changes May 13, 2024
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Need to propagate the name change / other changes (eg. no docker strategy) back to the template 👍🏻

drpatelh
drpatelh reviewed May 13, 2024
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@drpatelh drpatelh modified the milestones: 3.15.0, 3.16.0 May 29, 2024
@drpatelh drpatelh marked this pull request as draft May 29, 2024 10:55
pditommaso
pditommaso reviewed Jun 17, 2024
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nextflow.config
Comment on lines +260 to +261
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
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This should be removed otherwise it will cause the use of a docker container to be converted to singularity one ..

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also worth adding wave.build.conda.mambaImage = 'mambaorg/micromamba:1.5.8-lunar' to prevent containers changes quietly when the base image will change on wave side

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@pditommaso pditommaso pditommaso left review comments

@ewels ewels ewels approved these changes

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@maxulysse @ewels @pditommaso @adamrtalbot @drpatelh