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Fix dev branch root commit #28

Merged
merged 2 commits into from
May 13, 2024
Merged

Fix dev branch root commit #28

merged 2 commits into from
May 13, 2024

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scwatts
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@scwatts scwatts commented May 12, 2024

Notes

Background

  • the root commit of the master branch is missing from the dev branch
  • it is present in repo backups prior to nf-core transfer, so something went wrong during prep/transfer

Changes

  • this PR replays history of the master branch in dev
  • the end effect is just to add the root commit to dev
  • history is well preserved since only a single commit is been prepended to dev history
  • no ref breakage to existing GH issues, PRs, etc

Other

@maxulysse is this an acceptable way to fix this problem? Are there other considerations I need to make here?

I really don't want to rebase dev on top of master and potentially lose linkage with existing references, and this is a reasonable approach as far as I can tell.

The root commits of master and TEMPLATE are also different but I seem to already have merged TEMPLATE with dev for the nf-core/tools template PRs, so that commit history will be propogated to master at the first release.

This is painfully messy, apologies!

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/oncoanalyser 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@scwatts scwatts requested a review from maxulysse May 12, 2024 10:16
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github-actions bot commented May 12, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 77f8074

+| ✅ 175 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  57 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.3.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config
  • system_exit - System.exit in main.nf: System.exit(1) [line 45]
  • system_exit - System.exit in main.nf: System.exit(1) [line 46]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]
  • system_exit - System.exit in WorkflowOncoanalyser.groovy: System.exit(1) [line 62]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 29]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 39]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 47]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 55]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 63]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 68]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 84]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 89]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 108]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 113]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 121]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 182]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 264]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 276]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 284]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 291]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 299]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 314]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 335]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 346]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 355]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 385]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 118]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 125]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 132]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 146]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 156]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 161]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 174]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 190]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 199]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 210]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 220]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-12 10:17:11

@scwatts scwatts merged commit 50fe58e into dev May 13, 2024
4 checks passed
@scwatts scwatts deleted the fix-dev-root-commit branch May 13, 2024 08:59
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@maxulysse maxulysse maxulysse approved these changes

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@scwatts @maxulysse