8000 Fix join issues in ME calling subworkflow by ramprasadn · Pull Request #556 · nf-core/raredisease · GitHub
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Fix join issues in ME calling subworkflow #556

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Merged
merged 5 commits into from
May 23, 2024
Merged

Fix join issues in ME calling subworkflow #556

merged 5 commits into from
May 23, 2024

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ramprasadn
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PR checklist

Fixes #542

  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@ramprasadn ramprasadn changed the base branch from master to dev May 23, 2024 12:10
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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 @ramprasadn,

It looks like this pull-request is has been made against the nf-core/raredisease 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/raredisease 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.

Thanks again for your contribution!

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github-actions bot commented May 23, 2024 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e7f16d2

+| ✅ 183 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-23 12:24:51

@ramprasadn ramprasadn requested review from fa2k and jemten May 23, 2024 12:21
@ramprasadn ramprasadn marked this pull request as ready for review May 23, 2024 12:25
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fa2k commented May 23, 2024

This works well for me (1) running the code with skip_me_calling enabled, and (2) get a "missing parameter" message if I don't enable skip_me_calling. The code looks good to me. Thanks for a nice and quick fix :)

fa2k
fa2k approved these changes May 23, 2024
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Thanks for the review @fa2k!

@ramprasadn ramprasadn merged commit 4d1c398 into dev May 23, 2024
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@ramprasadn ramprasadn mentioned this pull request May 23, 2024
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@ramprasadn ramprasadn deleted the me_required_files branch May 28, 2024 08:24
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@fa2k fa2k fa2k approved these changes

@jemten jemten Awaiting requested review from jemten

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Join error ME_INDEX_SPLIT_ALIGNMENT
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