Run CI tests that use GitHub secrets (i.e. email address and NCBI key for protein download from NCBI) also on pushes on dev branch and on PRs that are not from forks. These tests can not be run on PRs from forks, since secrets can not be accessed from forks. Before these tests were run only on commits on master, but it would be good to test also this part of the pipeline more often.
Note that one now has to explicitly check if these tests fail, since it does not appear before merging!
Additionally, I replaced the first test with test_assembly_only, since the test profile also requires secrets. We can clean this up in the future, when the tests are complete (I created a reminder https://github.com/nf-core/metapep/issues/41).
PR checklist
[x] 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/metapep 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).
Run CI tests that use GitHub secrets (i.e. email address and NCBI key for protein download from NCBI) also on pushes on dev branch and on PRs that are not from forks. These tests can not be run on PRs from forks, since secrets can not be accessed from forks. Before these tests were run only on commits on master, but it would be good to test also this part of the pipeline more often. Note that one now has to explicitly check if these tests fail, since it does not appear before merging!
Additionally, I replaced the first test with
test_assembly_only
, since thetest
profile also requires secrets. We can clean this up in the future, when the tests are complete (I created a reminder https://github.com/nf-core/metapep/issues/41).PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).