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Update pretext version#368

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weaglesBio merged 4 commits intodevfrom
update_pretext
Mar 5, 2025
Merged

Update pretext version#368
weaglesBio merged 4 commits intodevfrom
update_pretext

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@weaglesBio weaglesBio commented Feb 28, 2025

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).

Update pretext singularity version to pretext:0.0.8-yy5-c1

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github-actions bot commented Feb 28, 2025

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 @weaglesBio,

It looks like this pull-request is has been made against the sanger-tol/treeval 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 sanger-tol/treeval 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!

@weaglesBio weaglesBio changed the base branch from main to dev February 28, 2025 15:29
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github-actions bot commented Feb 28, 2025 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5be44eb

+| ✅ 126 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.2'
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • 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 ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2025-03-03 15:09:48

@DLBPointon DLBPointon linked an issue Mar 3, 2025 that may be closed by this pull request
[KNOWN BUG] PretextGraph sometimes generates a malformed graph upon ingestion #359
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DLBPointon
DLBPointon approved these changes Mar 3, 2025
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Once the log is deleted, merge away.

@weaglesBio weaglesBio merged commit d10846e into dev Mar 5, 2025
6 checks passed
@DLBPointon DLBPointon deleted the update_pretext branch March 12, 2025 14:29
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@DLBPointon DLBPointon DLBPointon approved these changes

@yumisims yumisims Awaiting requested review from yumisims

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[KNOWN BUG] PretextGraph sometimes generates a malformed graph upon ingestion

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@weaglesBio @DLBPointon