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Status inference update #1177

Merged
merged 4 commits into from
Aug 15, 2023
Merged

Status inference update #1177

merged 4 commits into from
Aug 15, 2023

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FriederikeHanssen
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Close #1175

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/sarek 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 Aug 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7d27bf6

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-15 07:55:31

@asp8200
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asp8200 commented Aug 8, 2023

Do we have a pytest checking that this status-issue is fixed and doesn't re-emerge? If not, then I guess it should be possible to check for this in the output from some of the pytests which use tests/csv/3.0/mapped_joint_bam.csv.

@FriederikeHanssen
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Do we have a pytest checking that this status-issue is fixed and doesn't re-emerge? If not, then I guess it should be possible to check for this in the output from some of the pytests which use tests/csv/3.0/mapped_joint_bam.csv.

Yes, please see the adjusted test file.

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asp8200 commented Aug 15, 2023

Do we have a pytest checking that this status-issue is fixed and doesn't re-emerge? If not, then I guess it should be possible to check for this in the output from some of the pytests which use tests/csv/3.0/mapped_joint_bam.csv.

Yes, please see the adjusted test file.

Yes, I did notice that, and I know that csv-file is used for input on some tests. So if this status-inference doesn't work, then something in, say, this test will fail?

@FriederikeHanssen FriederikeHanssen merged commit 38c57e6 into nf-core:dev Aug 15, 2023
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

@maxulysse maxulysse maxulysse approved these changes

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