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Singularity bugfix: keep report log file list in local workdir #223

Merged
merged 1 commit into from
Jan 27, 2023
Merged

Singularity bugfix: keep report log file list in local workdir #223

merged 1 commit into from
Jan 27, 2023

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dladd
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@dladd dladd commented Jan 17, 2023

Tiny bugfix for airrflow/reveal:

I was getting file-not-found errors for the temporary log file in the REPORT_FILE_SIZE step. Pretty sure this was a singularity bind mounts issue from leaving the log file list in the global workDir instead of the process-specific local dir. The commit below seems to work around this without issue.

Thanks and happy 2023!

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/airrflow 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).

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github-actions bot commented Jan 17, 2023 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 6867001

+| ✅ 153 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

❗ Test warnings:

  • pipeline_todos - TODO string in airrflow.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-01-17 23:50:19

@ggabernet ggabernet changed the base branch from airrflow to dev January 27, 2023 12:21
@ggabernet ggabernet changed the base branch from dev to airrflow January 27, 2023 12:21
ggabernet
ggabernet approved these changes Jan 27, 2023
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Thanks @dladd! That seems indeed a more elegant solution here. I've retriggered the tests and if all of them pass I will merge!

@ggabernet ggabernet merged commit 1cb54f3 into nf-core:airrflow Jan 27, 2023
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@ggabernet ggabernet ggabernet approved these changes

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@dladd @ggabernet