Nf schema - #263
Open
DLBPointon wants to merge 6 commits into
Open
Conversation
This PR is against the
|
|
❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
muffato
reviewed
Aug 31, 2026
| // Nextflow plugins | ||
| plugins { | ||
| id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet | ||
| id 'nf-schema@2.7.2' // Validation of pipeline parameters and creation of an input channel from a sample sheet |
Member
There was a problem hiding this comment.
Can we avoid this ? 2.7.2 forces Nextflow 26.04 as the minimum version
Contributor
Author
There was a problem hiding this comment.
I don't think so, pretty sure 2.7.2 is the first version that supports casting.
We can keep it the current way at the minute, i will just need to have a branch for ASCC until, maybe, the next template update?
Member
There was a problem hiding this comment.
toBoolean() is a native Groovy method. It's not from nf-schema. The changes should work with nf-schema 2.5.1
Contributor
Author
There was a problem hiding this comment.
Just had a look again, yeah you don't need the toBoolean(). That's a hang over from me trying a couple of things at the same time.
You need the 2.7.2 to cast the params to their proper type to pass validation.
Using the toBoolean() would effect the params after validation.
I guess either way could work.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changes related to updating nf-schema to allow booleans to work on the cli again.
This change is needed for ASCC.
Allows cli args to be cast to their config defined type.
Also removed an unused ch_versions from Input_check whilst I was mucking around.