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Nf core template merge 2.13 resolve conflicts #78

Merged
merged 2 commits into from
Mar 7, 2024
Merged

Nf core template merge 2.13 resolve conflicts #78

merged 2 commits into from
Mar 7, 2024

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asp8200
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@asp8200 asp8200 commented Feb 21, 2024 •
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My attempt at merging dev into template and back again into dev - hopefully resolving conflicts.

Both profile=test and profile=test_full are passing.

Not sure the way the params.fasta and params.fasta_fai are handled is completely correct.

Also, when I run the pipeline in test-mode, I get

WARN: Access to undefined parameter `fasta_fai` -- Initialise it to a default value eg. `params.fasta_fai = some_value`
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

All CI-tests (except linting) are passing 🥳 Thanks, @maxulysse 🫶

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github-actions bot commented Feb 21, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 254d231

+| ✅ 165 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   7 tests had warnings |!
-| ❌   3 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • schema_params - Default value for param fasta_fai invalid: Not in pipeline parameters. Check nextflow.config.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.1.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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!
  • schema_params - Schema param fasta_fai not found from nextflow config

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-07 09:43:02

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Version 2.13.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #80

Please use #80 to merge in the new changes from the nf-core template as soon as possible.

@maxulysse maxulysse reopened this Mar 7, 2024
@maxulysse maxulysse marked this pull request as ready for review March 7, 2024 09:42
@maxulysse maxulysse merged commit c1a9383 into nf-core:dev Mar 7, 2024
34 of 36 checks passed
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asp8200 commented Mar 7, 2024

@maxulysse : How about those questions concerning params.fasta and params.fasta_fai in the description of the PR?

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@asp8200 @nf-core-bot @maxulysse