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Allow tarballed inputs instead of only directories #61

Merged
merged 21 commits into from
Dec 20, 2023
Merged

Allow tarballed inputs instead of only directories #61

merged 21 commits into from
Dec 20, 2023

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fasterius
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@fasterius fasterius commented Dec 20, 2023 •
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PR checklist

This work-in-progress PR contains changes to that allows using tarballed (.tar.gz) input instead of just local directories, which allows testing to work properly out-of-the-box. Previous testing worked using GitHub actions where the test dataset was downloaded prior to running nf-test-based tests, but this did not work using test profile, which this PR remedies.

  • This comment contains a description of changes (with reason).
  • If necessary, also make a PR on the nf-core/spatialtranscriptomics branch on the nf-core/test-datasets repository. A work-in-progress version of the test data is available at fasterius/test-datasets.
  • Change the test data location from fasterius/test-datasets to nf-core/test-datasets in the code.
  • 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.
  • CHANGELOG.md is updated.
  • Remove the GitHub Actions CI that downloads the test data prior to execution once remote test data is working correctly for all tests.

fasterius and others added 13 commits December 18, 2023 14:21
@fasterius
Add .nf-test* to .gitignore
cb0e10f
@fasterius
Use compressed tarball for downstream test data
a9d0214 
Use a compressed tarball of the downstream (post-Space Ranger) test data
as a workaround of not being able to stage a remote directory.
@fasterius
Remove old run_spaceranger parameter mention
f567498
@fasterius
Clarify test profile description
3d08dd6
@fasterius
Use remote files for nf-test downstream test
00185fb
@fasterius
Update nf-test snapshot
0e51ef3
@fasterius
Use channel branching to check input type
152f0fd 
Use channel branching to check the input type (directory or tarball) of
post-Space Ranger input instead of checking for the `test` profile. This
is more generalisable and a better overall solution to the problem of
different input types.
@fasterius
Add info on tarball input in usage docs
f248416
@fasterius
Use compressed tarball of Space Ranger test data
2b35764
@fasterius
Add info on Space Ranger tarball input in docs
5ae23b0
@fasterius
Update downstream nf-test tests
1c9ad18
@nf-core-bot
Template update for nf-core/tools version 2.11
a7dc216
@fasterius
Update Space Ranger nf-test pipelines
fabdc22
@fasterius fasterius self-assigned this Dec 20, 2023
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github-actions bot commented Dec 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4a06e97

+| ✅ 158 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 output.md: More details for each analytical step should probably be added,
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowSpatialtranscriptomics.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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.11
  • Run at 2023-12-20 12:36:38

@fasterius fasterius marked this pull request as ready for review December 20, 2023 12:46
@fasterius fasterius merged commit 04e4568 into dev Dec 20, 2023
8 checks passed
@fasterius fasterius deleted the tests branch December 20, 2023 12:46
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