Closed apeltzer closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 7b37e90
+| ✅ 190 tests passed |+
#| ❔ 3 tests were ignored |#
!| ❗ 7 tests had warnings |!
We are looking into this issue with @atrigila. For the utils_nfvalidation_plugin, the issue seems to be with where the output was expected to be located when writing the nf-tests. The utils_nfvalidation_plugin/main.nf uses this line to print the help message: This gets printed into the nextflow.log, but not into stdout:
One alternative to fix this would be to replace the log.info with a println, this way the output will be redirected to stdout insted of to the nextflow.log:
@apeltzer An alternative would be to re write the nf-tests so that they check the nextflow.log, or something similar. What do you think?
No strong opinion... I think it's fine (or even preferable) if help is written to STDOUT (most CLI tools do that). Have you checked what other pipelines do?
Variantbenchmarking / taxprofiler both use the unmodified utils_nfvalidation_plugin/main.nf
@apeltzer @grst I think using log instead of println is better, the log message sticks a little longer in the terminal than println, making it easier to read, besides that, you get it printed in a different color which also helps visibility, but you can do that with println too, so not the biggest advantage. I'm not sure why the nf-tests were passing before for this subworkflow, could it be that they weren't being properly executed? I'll create an issue in the modules repo
The nf-validation plugin does not have a snapshot, therefore, I don't know if we can say that these tests were working before.
OK - lets stick with nf-validation
for now, the bug (or whatever it in the end turns out to be) was reported upstream and is probably tackled when nf-core moves towards wider usage of nf-schema in favor of nf-validation, thus also updating the required subworkflows / replace them entirely.
@apeltzer @atrigila @grst Removed workflow testing from CI to avoid running the tests on the subworkflows, because UTILS_NEXTFLOW_PIPELINE and UTILS_NFVALIDATION_PLUGIN have nf-tests that are not working. The reason for them failing has been documented and an issue was opened: https://github.com/nf-core/modules/issues/6166. These failing nf-tests don't seem to have any impact on the disambiguate pipeline, so they have been disabled in this PR, to prepare the dev branch for release. We will update the CI tests once the issue with the subworfklows is sorted out.
So its just the downloading feature failing now - filed an issue for that one: https://github.com/nf-core/tools/issues/3111
@apeltzer @atrigila I created a PR for the comments left in this review, not sure if we are going to merge them in this release, but to get the ball rolling in case we do: https://github.com/nf-core/demultiplex/pull/248/files
Adding here "just" the points addressed in this release 👇🏻
1.5.0 - 2024-08-12
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