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Adding foldseek to the workflow #185

Merged
merged 16 commits into from
Oct 8, 2024
Merged

Adding foldseek to the workflow #185

merged 16 commits into from
Oct 8, 2024

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ziadbkh
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@ziadbkh ziadbkh commented Oct 8, 2024

Still needs few changes

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/proteinfold 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).

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github-actions bot commented Oct 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d5d4ef5

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • nextflow_config - Config manifest.version should end in dev: 1.1.1
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-10-08 12:03:15

JoseEspinosa
JoseEspinosa approved these changes Oct 8, 2024
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@JoseEspinosa JoseEspinosa left a comment •
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Nice job! There are a couple of things that I will modify in a new PR, by the moment I will merge this one in dev without taking into account the nf-core linting as we need to synchronize the template for the new tools version 3.0.0

main.nf
@@ -206,6 +207,24 @@ workflow NFCORE_PROTEINFOLD {
)
ch_versions = ch_versions.mix(GENERATE_REPORT.out.versions)
}

if (params.foldseek_search == "easysearch"){
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Are there plans to implement other foldseek modules such as multimersearch ?

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@JoseEspinosa JoseEspinosa merged commit b3ecf98 into nf-core:dev Oct 8, 2024
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@ziadbkh @JoseEspinosa