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Fix WES error #578

Merged
merged 2 commits into from
Jul 1, 2024
Merged

Fix WES error #578

merged 2 commits into from
Jul 1, 2024

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ramprasadn
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PR checklist

There is a conditional that ensure that CNVnator and TIDDIT are not run on WES samples, but their version collect statements were outside of those conditionals which resulted in errors for WES samples. This PR fixes that.

  • 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).

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github-actions bot commented Jul 1, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit bcc23b2

+| ✅ 185 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 2024-07-01 10:29:48

@ramprasadn ramprasadn marked this pull request as ready for review July 1, 2024 10:47
fellen31
fellen31 approved these changes Jul 1, 2024
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👍

jemten
jemten approved these changes Jul 1, 2024
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👍

@ramprasadn ramprasadn merged commit ea493a7 into dev Jul 1, 2024
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@ramprasadn ramprasadn deleted the wes_fix branch July 4, 2024 07:30
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@fellen31 fellen31 fellen31 approved these changes

@jemten jemten jemten approved these changes

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@ramprasadn @jemten @fellen31