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Fix igenomes_base in nextflow_schema #479

Merged
merged 2 commits into from
Oct 16, 2024
Merged

Fix igenomes_base in nextflow_schema #479

merged 2 commits into from
Oct 16, 2024

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nschcolnicov
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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/smrnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines 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).

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github-actions bot commented Oct 15, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 45e3a40

+| ✅ 243 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.fastp_known_mirna_adapters

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-16 15:04:29

@nschcolnicov
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Removed the igenomes_base from the nextflow schema, not sure why the CI test checking if the PR is pointing towards dev is failing, should be ok

mashehu
mashehu reviewed Oct 15, 2024
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@mashehu mashehu left a comment

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Are you not using igenomes?

@nschcolnicov
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Are you not using igenomes?

Yes we are, igenomes_base was added into the nextflow_schema as a quickfix, I'm reverting this fix which is no longer needed. With the recent update in the nf-core template, the parameters from schema ignore were not being properly parsed, making the linting fail due to not seeing an entry for the igenomes_base parameter in the nextflow_schema. This was already patched, so we no longer need to have the igenomes_base entry in the nextflow_schema

@mashehu
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mashehu commented Oct 16, 2024

but if you use igenomes, why don't you want to use igenomes_base? it is a standard param when including igenomes in the template.

@nschcolnicov
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but if you use igenomes, why don't you want to use igenomes_base? it is a standard param when including igenomes in the template.

We want to use igenomes_base and we are using igenomes_base. We just don't need to have it the schema, but we still have it as a parameter.

https://nfcore.slack.com/archives/CL66GAJBF/p1729006915504669

@mashehu
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mashehu commented Oct 16, 2024

the schema should cover every parameter

@nschcolnicov nschcolnicov changed the title remove value from schema Fix igenomes_base Oct 16, 2024
@nschcolnicov nschcolnicov changed the title Fix igenomes_base Fix igenomes_base in nextflow_schema Oct 16, 2024
@nschcolnicov
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@mashehu Should be good to go now, let me know if you have any comments

@mashehu mashehu merged commit 3b7df98 into dev Oct 16, 2024
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@mashehu mashehu mashehu approved these changes

@atrigila atrigila Awaiting requested review from atrigila

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@nschcolnicov @mashehu