Hi @Bilal Asser, just left a comment on issue #13, want to try adding

storeDir

to the BBDUK step. Would appreciate a pointer to where the test profile config lives when you get a chance.

Hi @Nkiruka Efenji Creating one would be a great idea/help! Right now I have been setting the

bbduk

speed to 12 locally when I can't use

-resume

nextflow.config

only has the following

include

lines:

includeConfig 'conf/modules.config'

includeConfig 'nextflow.custom.config'

. And as I'm getting to know the template structure, I am realising there is even some redundancy in

nextflow.custom.config

so maybe start there if the

debug

profile in

nextflow.config

doesn't suit and you have to write new stuff. Then we will always have to see what default configuration makes sense before the first PR to

main

anyway.

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There should not have been any compilation from this call.

This is really helpful! I am wrapping up a deadline this week, so I will dig into

nextflow.custom.config

and the

debug

profile once that's done, will update here once I have had a proper look.

Grateful for any contributions, cheers 👍 good luck with your deadline