Hi. We are in the process of upgrading nf-core tools and pipelines from version

3.2.1

to

3.3.2

. Seeing an error when running

nf-core pipelines lint --release

command

included_configs: Pipeline config does not include custom configs. Please uncomment the includeConfig line.

We do not have any custom pipeline configs. In version

3.2.0

, above error used to be a warning and now it is an error. To test this out, did the following -- • Created a nf-core pipeline from scratch using the nf-core tools cli (

nf-core pipelines create

) and using the defaults it presented on the terminal UI (version 1.0.0dev). • Ran

nf-core pipelines lint

. It passed without issues. • Issued a

nf-core pipelines bump-version 1.0.0

• Ran the lint command again with '--release' option -->

nf-core pipelines lint --release

. It fails with the error above regarding the included_configs. It seems to me -- that it is a bug with the new

3.3.2

version. Would anyone be able to confirm the behavior so that I can request a bug fix? Our current (only) way of working around this issue is to add

included_configs: False

in the .nf-core.yml (which we don't want to do). Please help. If this is not the correct channel to ask/report this -- please let me know as well.

When you set up the pipeline, did you specify it was a nf-core pipeline or an external one?

I set it up as an nf-core pipeline.

I have a feeling maybe you've set the former rather than the latter? The linting should skip for the latter because custom configs are automatically made for nf-core pipelines

image.png

Yeah switch

is_nf-core

to false if this is not an accepted nf-core pipeline

ok. let me try that quickly

Yes, I don't think external pipelines are meant to use the release flag as you don't release on our infrastructure

Hmm. ok. We were under the impression that '--release' flag is a step to double-check things upon tagging a main branch version and creating a release in GitHub.

It may have changed over the years then, there defiitely used to be nf-core specific things (docker image tagging etc)

Thank you. I will ask.

hi! Jame's suggestion of setting the pipeline as non-nf-core sounds good 👍🏻 but to clarify the error you saw, this is because in the nextflow.config we have a line which is including the pipeline configuration https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/nextflow.config#L223 and this should be uncommented for nf-core pipelines

Thank you. We have used that workaround to skip the test for now for our production pipeline. So, is that the intended error/feature to fail upon release or bug that it should have been a warning?

it's expected. When you have the commented line it is a failure telling you to uncomment it, if the line is not present at all, then it is a warning

Thank you, Julia for that information.

Note that you can ctrl+click any of the CLI linting error names and jump to the docs for that error. In this case, here: https://nf-co.re/docs/nf-core-tools/api_reference/3.3.2/pipeline_lint_tests/included_configs