Closed adamrtalbot closed 7 months ago
nf-core lint
overall result: Failed :x:Posted for pipeline commit 35463cb
+| ✅ 158 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 1 tests had warnings |!
-| ❌ 4 tests failed |-
Errr help. I haven't changed that much stuff here, it shouldn't be failing this badly?
@adamrtalbot thanks for figuring out the issue with the nextflow_config.yml
file. There's a new template update and that's why the nf-core lint tests are failing. And there seems to be a docker.userEmulation
deprecation for the Nextflow latest version and that's why the tests are failing for this version. I will commit a fix here so the CI tests pass, but I will do a template update in a separate PR. Also the change in indentation breaks the prettier linting.
Also the change in indentation breaks the prettier linting.
Doh, I need to fix that. Something up with my editor because this has happened before.
If you merge in the template update I can rebase this branch.
making @maxulysse happy
<3
The nextflow_schema.json used invalid JSON schema for clonal_threshold which accepts two types of values. This PR changes it to use the
oneOf
and some validation instead of a list.Fixes #292
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).