Batch update: copy max_* params to resourcelimit directive

[jfy133]

This is in preparation for the new nf-core/tools 3.0.0 release, that deprecates the check_max() function + max_() params with the native Nextflow 'resourceLimit' directive.

I have done an initial pass using a bash script, but there are some remaining profiles that need to be addressed.

This will need to be dealt with manually.

Done	Config	Issue
x	conf/alice.config	Multiple process blocks
x	conf/arcc.config	Multiple process blocks
x	conf/azurebatch.config	Multiple process blocks
x	conf/azurebatchdev.config	Multiple process blocks
x	conf/crg.config	Multiple process blocks
x	conf/czbiohub_aws.config	Multiple process blocks
x	conf/eva.config	Multiple process blocks
x	conf/hasta.config	Multiple process blocks
x	conf/hki.config	Multiple process blocks
x	conf/imperial.config	Multiple process blocks
x	conf/incliva.config	Multiple process blocks
x	conf/maestro.config	Multiple process blocks
x	conf/medair.config	Multiple process blocks
x	conf/pawsey_nimbus.config	Multiple process blocks
x	conf/rosalind_uge.config	Multiple process blocks
x	conf/sage.config	Multiple process blocks
x	conf/sanger.config	Multiple process blocks
x	conf/uge.config	Multiple process blocks
x	conf/uppmax.config	Multiple process blocks
x	conf/vsc_calcua.config	Multiple process blocks
x	conf/vsc_kul_uhasselt.config	Multiple process blocks
x	conf/vsc_ugent.config	Multiple process blocks
x	crukmi	Uses check_max()
x	rosalind_uge	Unused check_max()
x	sage	Uses check_max()
x	sahmri	Uses check_max()
x	uge	Unused check_max()
x	utd_ganymede	Uses check_max()

To be adressed in follow up PR

Done	Config	Issue
	pipeline/eager/eva	Uses check_max()
	pipeline/eager/maestro	Uses check_max()
	pipeline/eager/mag	Uses check_max()
	pipeline/rnafusion/hasta	Uses check_max()
	pipeline/taxprofiler/hasta	Uses check_max()

Scripts and log:
batch-resourcelimit-scripts.zip

[edmundmiller]

Go for it for my configs!

[mahesh-panchal]

I think the uppmax profile should have the full resource limits map set. I have a feeling inheritance doesn't apply here.

[jfy133]

@HaidYi I've had to tweak your St. Jude profile slightly to make the tests pass (not sure why it didn't come up in your original PR), it bascially uses a Groovy call to resolve the TMPDIR path, because otherwise Nextflow thinks it's it's own variable.

I hope that's OK

[JoseEspinosa]

LGTM! 🚀