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Fix two instances of wrong process name passed to ch_versions.mix() when running in sentieon mode #454

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merged 4 commits into from
Dec 18, 2023
Merged

Fix two instances of wrong process name passed to ch_versions.mix() when running in sentieon mode #454

merged 4 commits into from
Dec 18, 2023

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alkc
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@alkc alkc commented Dec 15, 2023 •
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This small update fixes two similar bugs where the wrong process name is passed in a call to ch_versions.mix() when run in sentieon mode.

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/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>).
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github-actions bot commented Dec 15, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f02e3f1

+| ✅ 151 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-18 13:45:15

jemten
jemten approved these changes Dec 15, 2023
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Nice catch @alkc and thanks for the PR!

@jemten jemten merged commit 4f961a0 into nf-core:dev Dec 18, 2023
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alkc commented Dec 20, 2023

Nice catch @alkc and thanks for the PR!

Glad to be able to help!

Speaking of sentieon, I've identified an issue in the nf-core sentieon dedup module that crashes the rd pipeline when trying to do a sentieon-mode stub run: nf-core/modules#4632

Should I document it as an issue in the raredisease issue tracker?

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jemten commented Dec 20, 2023

It's always nice to get it documented as an issue and very nice to see that you have a PR in modules to solve it. Once that PR is merged we can update the dedup module in the pipeline.

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alkc commented Dec 20, 2023

Done! #462

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