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Add singularity/apptainer warning #66

Merged
merged 3 commits into from
Oct 25, 2023
Merged

Add singularity/apptainer warning #66

merged 3 commits into from
Oct 25, 2023

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fbdtemme
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Add a warning and workaround for using Singularity/Apptainer with latest Nextflow.

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/pixelator 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).

@fbdtemme
Remove singularity/apptainer --writable-tmpfs flag.
6df3f7c 
This option does not fix the problem where the user home dir is not
mounted with singularity/apptainer executor because the
in-memory tmpfs partition is too small to store all data written.
@fbdtemme
Add warning for singularity/apptainer
8ba4a85 
Add a warning and workaround to the docs ( both README and USAGE) for
singularity/apptainer and Nextflow 23.10. This is needed because of
the change in 23.07.0-edge to no longer mount the home
directory when launching an Apptainer or singularity container.
@fbdtemme
Update CHANGELOG
2ed56e4
johandahlberg
johandahlberg approved these changes Oct 25, 2023
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Looks good.

@fbdtemme fbdtemme merged commit 2e1767b into dev Oct 25, 2023
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@fbdtemme fbdtemme deleted the add-singularity-warning branch October 25, 2023 15:27
@fbdtemme fbdtemme mentioned this pull request Oct 26, 2023
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@johandahlberg johandahlberg johandahlberg approved these changes

@ambarrio ambarrio Awaiting requested review from ambarrio

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2 participants
@fbdtemme @johandahlberg