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Dp24 module update 2 #335

Merged
merged 10 commits into from
Nov 21, 2024
Merged

Dp24 module update 2 #335

merged 10 commits into from
Nov 21, 2024

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DLBPointon
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Restarting this PR,

Fixing un-related merge conflicts led to a reversion with containers.

@DLBPointon DLBPointon added documentation Improvements or additions to documentation enhancement New feature or request labels Nov 21, 2024
@DLBPointon DLBPointon added this to the Release 1 milestone Nov 21, 2024
@DLBPointon DLBPointon self-assigned this Nov 21, 2024
@DLBPointon DLBPointon changed the base branch from dev to dp24_module_update_samtools November 21, 2024 11:55
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github-actions bot commented Nov 21, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ada598

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.2.0'
  • 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/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 2024-11-21 14:38:31

@DLBPointon
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DLBPointon commented Nov 21, 2024 •
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Ok so the updated BUSCO_BUSCO module is causing an issue on the runner

Update:

  • The only difference between the BUSCO and BUSCO_BUSCO module is that it is nested in a folder and the version moves from BUSCO v5.5 to v5.7.1.

  • Locally, the module is running fine. so I am unsure what is happening. We can patch this module to use 5.5 to see what happens.

@DLBPointon
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Confirmed that this is a v5.7 issue

@DLBPointon DLBPointon merged commit 85217d9 into dp24_module_update_samtools Nov 21, 2024
4 of 6 checks passed
@DLBPointon DLBPointon deleted the dp24_module_update_2 branch November 21, 2024 14:37
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