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Update config files and other minor code polishing #1325

Merged
merged 27 commits into from
Nov 10, 2023
Merged

Update config files and other minor code polishing #1325

merged 27 commits into from
Nov 10, 2023

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maxulysse
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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/sarek 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>).
  • 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).

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github-actions bot commented Nov 9, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 055818f

+| ✅ 143 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.0
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_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_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-10 09:33:51

FriederikeHanssen
FriederikeHanssen approved these changes Nov 9, 2023
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Changelog

@FriederikeHanssen
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Don't see anything changed with closures though

@maxulysse
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WIP, it's coming

@asp8200
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asp8200 commented Nov 9, 2023

Do you intend to include this PR in Sarek 3.4.0?

@maxulysse
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Do you intend to include this PR in Sarek 3.4.0?

Yes

FriederikeHanssen
FriederikeHanssen reviewed Nov 9, 2023
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looks good, but why remove the enabled?

conf/modules/modules.config Outdated Show resolved Hide resolved
@maxulysse
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looks good, but why remove the enabled?

we can't have closure with enabled, so converted to saveAs with which we can use closure

@maxulysse maxulysse changed the title Update config files Update config files and other minor code polishing Nov 9, 2023
@maxulysse maxulysse mentioned this pull request Nov 10, 2023
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@maxulysse maxulysse merged commit 51c7676 into dev Nov 10, 2023
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@maxulysse maxulysse deleted the config_update branch November 10, 2023 11:52
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@SPPearce SPPearce SPPearce approved these changes

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4 participants
@maxulysse @FriederikeHanssen @asp8200 @SPPearce