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Bugfix release 2.2.4 for mirtop gff issues #281

Merged
merged 16 commits into from
Oct 23, 2023
Merged

Bugfix release 2.2.4 for mirtop gff issues #281

merged 16 commits into from
Oct 23, 2023

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apeltzer
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@apeltzer apeltzer commented Sep 7, 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/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>).
  • 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 Sep 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4c27e8c

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSmrnaseq.groovy: Optionally add in-text citation tools to this list.

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-23 11:10:16

christopher-mohr
christopher-mohr approved these changes Sep 8, 2023
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LGTM if the bug pointed out in the other review is fixed. :)

@apeltzer
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@christopher-mohr @maxulysse @grst any idea what might cause this in test_full?

rror executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

@apeltzer apeltzer mentioned this pull request Sep 11, 2023
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@christopher-mohr @maxulysse @grst any idea what might cause this in test_full?

rror executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Is this still an issue? Is the full log available somewhere?

@apeltzer
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@christopher-mohr @maxulysse @grst any idea what might cause this in test_full?

rror executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Is this still an issue? Is the full log available somewhere?

I think it is, but I couldn't test the test_full profile on gitpod due to space / memory issues there. If we test somewhere else, should be possible to figure out whats going on there...

@christopher-mohr
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@christopher-mohr @maxulysse @grst any idea what might cause this in test_full?

rror executing process > 'NFCORE_SMRNASEQ:SMRNASEQ:MIRDEEP2:MIRDEEP2_RUN (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)


Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Is this still an issue? Is the full log available somewhere?

I think it is, but I couldn't test the test_full profile on gitpod due to space / memory issues there. If we test somewhere else, should be possible to figure out whats going on there...

Is it possible to trigger the corresponding Acton for this branch?

@lpantano
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happy to help here, is the idea to try to run the test_full and make sure it runs? If that, i can work on this.

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Addressing #289 here

@lpantano lpantano mentioned this pull request Oct 20, 2023
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@apeltzer
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Thanks @lpantano for chiming in here - I couldn't get back to this myself ...

@apeltzer apeltzer merged commit ed3d869 into dev Oct 23, 2023
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@apeltzer apeltzer deleted the fix-mirtop-gff branch October 23, 2023 12:09
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Yup Yup!

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@christopher-mohr christopher-mohr christopher-mohr approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@apeltzer @christopher-mohr @lpantano @maxulysse @tijeco