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Patch 1.2.1: Fix issue where pipeline fails on missing fields from NCBI datasets JSON #127

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merged 10 commits into from
Aug 1, 2024
Merged

Patch 1.2.1: Fix issue where pipeline fails on missing fields from NCBI datasets JSON #127

merged 10 commits into from
Aug 1, 2024

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tkchafin
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@tkchafin tkchafin commented Jul 8, 2024 •
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Closes #126

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
  • 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).

@tkchafin tkchafin linked an issue Jul 8, 2024 that may be closed by this pull request
ERROR pipeline failure when fields missing from NCBI genome report [v1.2.0] #126
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github-actions bot commented Jul 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e12d883

+| ✅ 132 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-07-12 11:02:07

@muffato muffato self-requested a review July 10, 2024 13:58
muffato
muffato reviewed Jul 10, 2024
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Good effort with the linting, @tkchafin, especially adding documentation for all the functions. But unfortunately, black disagrees and as you know, it's "opinionated" and "uncompromising" 😬 . We've got black installed on the farm in the nf-core Conda environments. That'll make the script comply with the CI.

Then, since we want to make a 1.2.1 release directly with this bugfix, please bump the version and update these files:

  • CHANGELOG.md
  • nextflow.config
  • CITATION.cff
    and change the target branch to main

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muffato commented Jul 10, 2024

(the "Run pipeline with test data" CIs now pass. That failure was transient)

@tkchafin tkchafin changed the base branch from dev to main July 12, 2024 10:09
muffato
muffato reviewed Jul 12, 2024
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Almost there !

CITATION.cff Outdated Show resolved Hide resolved
bin/create_table.py Outdated Show resolved Hide resolved
tkchafin and others added 2 commits July 12, 2024 11:59
@tkchafin @muffato
Update CITATION.cff
4e5ec7d 
Co-authored-by: Matthieu Muffato <[email protected]>
@tkchafin @muffato
Update bin/create_table.py
e12d883 
Co-authored-by: Matthieu Muffato <[email protected]>
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Also note that currently we are still using nan values as default for all fields. We had discussed using 0 for numeric fields (# chromosomes etc), so I can change it, although I like nan since that covers the case that a value is non-zero but erroneously missing in NCBI

muffato
muffato approved these changes Jul 12, 2024
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Changes look good for me, but can you wait a tiny bit before merging ? We have multiple Zenodo DOIs for our pipelines, and I'm in conversation with them about unifying the DOIs first

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muffato commented Aug 1, 2024

Merging this as the DOI is actually correct

@muffato muffato merged commit 028ddae into sanger-tol:main Aug 1, 2024
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ERROR pipeline failure when fields missing from NCBI genome report [v1.2.0]
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