Cheaha strict syntax conversion

[lianov]

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name: cheaha profile

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Issue #1020

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@nvnieuwk : here is the requested PR. As a recap, currently the Nextflow VS Code plugin complains about line 66 with the message Config option 'process.queue' with type String cannot be assigned to value with type Closure

Please also note that I have not enabled .call() (yet) line 54 as I was attempting a fix for the warning above. Thanks!

As a note, if we can solve this here, I will still need to test the profile in our cluster before moving forward with the merge.

[pontus]

I think it's the plugin that's wrong here, queue should be fine as a closure.

And you don't need/shouldn't do call() - that would cause evaluation at the wrong time.

You can go ahead and try this on your cluster.

[nvnieuwk]

This will also still fail because the parameter is function closure now, you can directly move the closure to the input of queue instead of assigning it to a parameter. Assigning to a parameter here should be discouraged since the code is only used once

[pontus]

But that closure is called with the expected parameters, so I'm not sure why it should fail?

I agree there's no point in having it in params though (and having it there likely gives warnings about it that should be dealt with by telling nf-schema to ignore it).

[lianov]

Hey all - excellent, I will make these changes and test it in our cluster and update this PR asap. Especial thanks for the clarification that I can safely ignore the Nexflow plug-in message (and before submitting this PR I did actually try to just directly provide the closure but the plug-in message was still there which generated confusion).

Either thanks! Will update here soon.

[lianov]

@nvnieuwk : changes are made and tested with test profile of rnaseq and demo in our cluster. Both passed. Could you do a final review for a merge (I assume you can approve the PR?). Thanks!

Edit: some automated checks failing below but on other profiles - let me know if there is anything on this end to be addressed.

[jfy133]

@lianov can you try merging master into? I've just made a chance to the CI where failing other configs should not block your own test

[nvnieuwk]

LGTM!

[lianov]

@jfy133 : done - looks like some tests are still failing but the cheaha one went through (merging is still blocked though).

[jfy133]

@jfy133 : done - looks like some tests are still failing but the cheaha one went through (merging is still blocked though).

Yeah, this will take time - but at least we confirm Cheaha passes, so we can force merge for you!