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Clean eval workflow #81

Merged
merged 7 commits into from
Dec 14, 2023
Merged

Clean eval workflow #81

merged 7 commits into from
Dec 14, 2023

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luisas
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@luisas luisas commented Dec 13, 2023 •
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PR checklist

Update the eval workflow so it relies mainly on nf-core modules.

Closes #71

  • 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/multiplesequencealign 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 Dec 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9790ff8

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • 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
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • 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 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 WorkflowMultiplesequencealign.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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 output.md: Write this documentation describing your workflow's output

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-14 07:42:44

JoseEspinosa
JoseEspinosa requested changes Dec 13, 2023
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LGTM! Just same small suggestions and question

subworkflows/local/evaluate.nf Outdated Show resolved Hide resolved
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subworkflows/local/align.nf
@@ -13,7 +13,6 @@ include { MUSCLE5_SUPER5 } from '../../modules/nf-core/musc

// Include local modules
include { CREATE_TCOFFEETEMPLATE } from '../../modules/local/create_tcoffee_template'
include { MTMALIGN_ALIGN } from '../../modules/local/mtmalign_align'
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Why this one is dropped?

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Because in the current version is not actually supported - Leon is working on that, so whenever it is ready we can add it back with the right nf-core import :)

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Fair enough, did not realized it was a local one

luisas and others added 3 commits December 14, 2023 08:41
@luisas @JoseEspinosa
Update subworkflows/local/evaluate.nf
9f330c6 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@luisas @JoseEspinosa
Update subworkflows/local/evaluate.nf
32ec041 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
@luisas @JoseEspinosa
Update subworkflows/local/evaluate.nf
9790ff8 
Co-authored-by: Jose Espinosa-Carrasco <[email protected]>
JoseEspinosa
JoseEspinosa approved these changes Dec 14, 2023
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Awesome! 😄

@JoseEspinosa JoseEspinosa merged commit a9a0317 into dev Dec 14, 2023
6 checks passed
@luisas luisas deleted the eval branch April 15, 2024 08:35
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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Restructure EVAL workflow
2 participants
@luisas @JoseEspinosa