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POC contrasts csv -> yaml #382

Merged
merged 10 commits into from
Dec 20, 2024
Merged

POC contrasts csv -> yaml #382

merged 10 commits into from
Dec 20, 2024

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nschcolnicov
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Addresses #370

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/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@nschcolnicov nschcolnicov mentioned this pull request Dec 9, 2024
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github-actions bot commented Dec 9, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34ca6ec

+| ✅ 300 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-20 14:03:35

nschcolnicov
nschcolnicov commented Dec 9, 2024
View reviewed changes
bin/validate_fom_components_yaml.R
@@ -0,0 +1,208 @@
#!/usr/bin/env Rscript
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Not a new file, created from https://github.com/pinin4fjords/shinyngs/blob/develop/exec/validate_fom_components.R

@grst grst mentioned this pull request Dec 10, 2024
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@nschcolnicov nschcolnicov marked this pull request as draft December 11, 2024 12:36
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

This was referenced Dec 18, 2024
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@nschcolnicov
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We should keep the bin/ script until we finish deciding on how the .yaml file will look like, I opened this issue to update the shinyngs package once that is settled: pinin4fjords/shinyngs#67, pinin4fjords/shinyngs#68

Current format supported by this POC is:

contrasts:
  - id: genotype_celltype_t1_t2
    comparison: ["Celltype", "T1", "T2"]

  - id: genotype_celltype_t1_FoB
    comparison: ["Celltype", "T1", "FoB"]

  - id: genotype_celltype_t1_MZ_fakeBatch
    comparison: ["Celltype", "T1", "MZ"]
    blocking_factors: ["fakeBatch"]

  - id: fakebatch_fakeBatch_b1_b2
    comparison: ["fakeBatch", "b1", "b2"]

@grst grst mentioned this pull request Dec 19, 2024
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@nschcolnicov nschcolnicov changed the base branch from dev to dev_tmp December 20, 2024 13:11
@nschcolnicov nschcolnicov marked this pull request as ready for review December 20, 2024 13:49
@nschcolnicov nschcolnicov merged commit ec554b2 into dev_tmp Dec 20, 2024
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