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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Make the configurations more readable. #19

Closed Mxrcon closed 3 years ago

Mxrcon commented 3 years ago

This task stems from https://github.com/emilyncosta/mtbseq-nf/pull/17#issuecomment-883365354

abhi18av commented 3 years ago

Then, let's try to use the following pattern

TBBWA {
// global params

// module params

// <- Here we add the module level params mentioned in tbbwa.nf file, which a user can override through a central location ->
resultsDir = "${params.outdir}/tbbwa"
saveMode = 'copy'
shouldPublish = true
}

I think that we're at a stage we can try some stuff out, I'd be curious to see how the params.outdir behaves within this context.

abhi18av commented 3 years ago

@Mxrcon , perhaps we can classify the changes mentioned https://github.com/emilyncosta/mtbseq-nf/issues/19#issuecomment-885039728 as part of pipeline params - what are you thoughts?

Mxrcon commented 3 years ago

Hmm, could be a task right? I agreed, the optional params acomodation still a great task

abhi18av commented 3 years ago

Agreed, I have create another task for params.

Closing this issue as the conf files are updated now.