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Fix mirtrace staging bug #335

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merged 5 commits into from Apr 3, 2024
Merged

Fix mirtrace staging bug #335

merged 5 commits into from Apr 3, 2024

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apeltzer
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@apeltzer apeltzer commented Apr 3, 2024

This addresses the staging / casting issue first identified in the issue #327

The previous fix ignored the possibility that (depending on the platform), directly referencing work directories can cause trouble as there is no guarantee that these are staged properly to the work dir of mirtrace. This is resolved by reverting to the previously working approach with mirtrace where the files are staged to the same directory, then adding functionality to use the filename(s) of provided files in the work dir of mirtrace directly instead. This ensures nextflow is aware of any files being staged to mirtrace, thus guaranteeing that files are properly staged.

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/smrnaseq 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).

@apeltzer apeltzer changed the base branch from master to dev April 3, 2024 08:19
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github-actions bot commented Apr 3, 2024

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @apeltzer,

It looks like this pull-request is has been made against the nf-core/smrnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/smrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

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github-actions bot commented Apr 3, 2024 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5d3b78f

+| ✅ 181 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-03 08:56:43

grst
grst approved these changes Apr 3, 2024
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LGTM

The filenames per sample are unique, right? So we shouldn't get any issues from staging them into the same directory.

@apeltzer apeltzer marked this pull request as ready for review April 3, 2024 08:54
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apeltzer commented Apr 3, 2024

LGTM

The filenames per sample are unique, right? So we shouldn't get any issues from staging them into the same directory.

Yes, they are - this should be fine 👍🏻

@apeltzer apeltzer merged commit 18d4eba into dev Apr 3, 2024
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@apeltzer apeltzer deleted the fix-mirtrace-staging-bug branch April 3, 2024 09:20
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@grst grst grst approved these changes

@christopher-mohr christopher-mohr Awaiting requested review from christopher-mohr

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@apeltzer @grst @fmalmeida