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Fix containerOptions with singularity #314

Merged
merged 1 commit into from
Mar 4, 2024
Merged

Fix containerOptions with singularity #314

merged 1 commit into from
Mar 4, 2024

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jonasscheid
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@jonasscheid jonasscheid commented Mar 4, 2024 •
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This fixes an issue introduced in #302. The aim was to imitate the depricated userEmulation . However, process.containerOptions is also used when specifying singularity profile and this obviously results in issues.

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.
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marissaDubbelaar
marissaDubbelaar approved these changes Mar 4, 2024
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LGTM

pontus
pontus approved these changes Mar 4, 2024
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One alternative could be setting docker.runOptions to the desired options, but this should work as well.

@jonasscheid jonasscheid merged commit daa4826 into nf-core:dev Mar 4, 2024
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@pontus pontus pontus approved these changes

@marissaDubbelaar marissaDubbelaar marissaDubbelaar approved these changes

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@jonasscheid @pontus @marissaDubbelaar