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.
[X] This comment contains a description of changes (with reason).
[X] 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.
[X] Change the test data location from fasterius/test-datasets to nf-core/test-datasets in the code.
[X] Make sure your code lints (nf-core lint).
[X] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[X] Usage Documentation in docs/usage.md is updated.
[X] CHANGELOG.md is updated.
[X] Remove the GitHub Actions CI that downloads the test data prior to execution once remote test data is working correctly for all tests.
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 runningnf-test
-based tests, but this did not work usingtest
profile, which this PR remedies.fasterius/test-datasets
tonf-core/test-datasets
in the code.nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.CHANGELOG.md
is updated.