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Fixing sentieon - code and tests #1469

Merged
merged 5 commits into from
Apr 17, 2024
Merged

Fixing sentieon - code and tests #1469

merged 5 commits into from
Apr 17, 2024

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asp8200
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@asp8200 asp8200 commented Apr 17, 2024 •
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TO-DO: Update changelog.

This PR should fix code and pytests related to Sentieon.

The change in the code is basically due to the fact that we now add meta to the channels for fasta and fai.

The tests now pass on DNGC's dev-HPC with a commercial Sentieon-license.

Note that the CI-tests for Sentieon are still disabled and won't be executed here on GitHub - due to the server with the test-license being down :-/

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 Apr 17, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 91f1ddf

+| ✅ 180 tests passed       |+
#| ❔  14 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.1
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/WorkflowSarek.groovy
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-17 14:17:26

@asp8200 asp8200 marked this pull request as ready for review April 17, 2024 13:32
@asp8200 asp8200 merged commit 0bf83b1 into dev Apr 17, 2024
44 checks passed
@maxulysse maxulysse deleted the fixing_sentieon branch April 25, 2024 09:21
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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@asp8200 @maxulysse @edmundmiller