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Dp24 jbrowse only #307

Merged
merged 21 commits into from
Nov 15, 2024
Merged

Dp24 jbrowse only #307

merged 21 commits into from
Nov 15, 2024

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DLBPointon
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This Re-adds the lib folder that got deleted?

Implements the JBrowse only subworkflow, I have confirmed this to work locally.

@DLBPointon DLBPointon added the enhancement New feature or request label Jul 12, 2024
@DLBPointon DLBPointon self-assigned this Jul 12, 2024
@DLBPointon DLBPointon linked an issue Jul 12, 2024 that may be closed by this pull request
JBrowse only workflow #305
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github-actions bot commented Jul 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 919a7f6

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

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.1.1'
  • 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 2024-11-15 15:20:30

@DLBPointon DLBPointon linked an issue Jul 16, 2024 that may be closed by this pull request
Reformat_intersect needs version output #309
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@DLBPointon DLBPointon linked an issue Jul 18, 2024 that may be closed by this pull request
Add No Conda support notices #308
Closed
@DLBPointon
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There were a further 2 modules using the no longer available quay.io/sanger-tol/cram-filter... container.

Now corrected.

weaglesBio
weaglesBio approved these changes Nov 15, 2024
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Only minor text changes

modules/local/fkutils/fkprof/main.nf Show resolved Hide resolved
modules/local/cram_filter_minimap2_filter5end_fixmate_sort.nf Show resolved Hide resolved
@DLBPointon DLBPointon merged commit f7d9db2 into dev Nov 15, 2024
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@DLBPointon DLBPointon deleted the dp24_jbrowse_only branch November 15, 2024 16:02
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@weaglesBio weaglesBio weaglesBio approved these changes

@yumisims yumisims Awaiting requested review from yumisims

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Reformat_intersect needs version output Add No Conda support notices JBrowse only workflow
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