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Dp24 module update 3 #339

Merged
merged 13 commits into from
Nov 27, 2024
Merged

Dp24 module update 3 #339

merged 13 commits into from
Nov 27, 2024

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DLBPointon
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@DLBPointon DLBPointon commented Nov 25, 2024 •
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More updates to modules.

As far as I can tell, the only outstanding module is pyfasta, which I would like to move away from anyway due the fact it has been depreciated for the past 6 years.

I have written a Fasta splitter in FasMan, just testing it now. At the minute it splits files into an upper bound.

This also re-introduces BUSCO-5.7 because of the whole Anaconda thing. Will have to investigate why it was failing originally.

@DLBPointon DLBPointon added the enhancement New feature or request label Nov 25, 2024
@DLBPointon DLBPointon self-assigned this Nov 25, 2024
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github-actions bot commented Nov 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8cf822c

+| ✅ 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 2024-11-26 12:59:42

@DLBPointon
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DLBPointon commented Nov 26, 2024 •
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Changing the fasta splitter to seqtk split rather than fasman (which slows down in containers for some reason)

@weaglesBio weaglesBio merged commit 20045d6 into dev Nov 27, 2024
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@DLBPointon DLBPointon deleted the dp24_module_update_3 branch January 28, 2025 15:45
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@weaglesBio weaglesBio weaglesBio approved these changes

@yumisims yumisims Awaiting requested review from yumisims

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