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Template update cleanup #128

Merged
merged 6 commits into from
Jan 30, 2024
Merged

Template update cleanup #128

merged 6 commits into from
Jan 30, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Jan 25, 2024 •
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Cleans up some broken things after the template update. Really need to fix the template updates. 😬

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github-actions bot commented Jan 25, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 6841c45

+| ✅ 158 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌  11 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.igenomes_base is set as s3://ngi-igenomes/igenomes in nextflow_schema.json but is s3://ngi-igenomes/igenomes/ in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-nascent_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nascent_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nascent_logo_dark.png does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.1
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in WorkflowNascent.groovy: Optionally add in-text citation tools to this list.
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-29 22:25:47

@edmundmiller edmundmiller changed the base branch from master to dev January 25, 2024 20:17
@edmundmiller edmundmiller self-assigned this Jan 25, 2024
@nf-core nf-core deleted a comment from github-actions bot Jan 29, 2024
@edmundmiller edmundmiller changed the title Template update Cleanup Template update cleanup Jan 29, 2024
@edmundmiller edmundmiller marked this pull request as ready for review January 29, 2024 22:24
CarsonJM
CarsonJM approved these changes Jan 30, 2024
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LGTM!

@edmundmiller edmundmiller merged commit a492c55 into dev Jan 30, 2024
3 of 7 checks passed
@edmundmiller edmundmiller deleted the template-cleanup branch February 14, 2024 03:41
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@CarsonJM CarsonJM CarsonJM approved these changes

@alyssa-ab alyssa-ab Awaiting requested review from alyssa-ab

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