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Cache data for GHA #933

Merged
merged 12 commits into from
Jan 27, 2023
Merged

Cache data for GHA #933

merged 12 commits into from
Jan 27, 2023

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maxulysse
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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/rnaseq 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 Jan 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1c3dcc1

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.10.1'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-01-27 12:09:17

@maxulysse maxulysse marked this pull request as ready for review January 27, 2023 11:17
drpatelh
drpatelh reviewed Jan 27, 2023
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nextflow_schema.json
},
"test_data_base": {
"type": "string",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3",
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Why rnaseq3 ?

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Created a subset of rnaseq which contains only the data actually used in the tests

drpatelh
drpatelh reviewed Jan 27, 2023
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.github/workflows/ci.yml
@@ -35,9 +35,33 @@ jobs:
with:
version: "${{ matrix.NXF_VER }}"

- name: Cache test data
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I could swear there was a way where we don't have to repeat this big block of code for every test?

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Probably, but we'll rewrote the tests soon enough, so we'll fix that in a future PR

@maxulysse
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BTW, this works the same and still pulls data from github.

nextflow run  maxulysse/nf-core_rnaseq -r cache_test_data -profile test,docker --outdir results

@maxulysse maxulysse merged commit ee0d80f into nf-core:dev Jan 27, 2023
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@drpatelh drpatelh drpatelh left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen @drpatelh