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georgiesamaha / configBuilder-nf

Nextflow config builder scripts for supported HPC infrastructures.
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Ask user if they want to set NXF_TEMP #48

Open georgiesamaha opened 8 months ago

georgiesamaha commented 8 months ago

Closes #23

jfy133 commented 8 months ago

Hm, this one we will need to think about/get feedback on. I think my original idea for this wasn't temp as in NXF_TEMP but rather scratch: https://www.nextflow.io/docs/latest/process.html#scratch That 'makes sense to me' (a local scratch/temp on a compute node), but I'm not sure what NXF_TEMP does... My feeling is that NXF_TEMP might be for the nextflow command itself, which is why it doesn't have a specific 'scope' equivalent and thus not be relevant for us here... Do you want to ask on the nextflow slack/discourse what the difference, and then we can update accordingly?

jfy133 commented 8 months ago

But otherwise (assuming it's OK to set NXF_TEMP): You could try auto0-detecting if NXF_TEMP is already set and use that to provide a default to the user (see my draft PR how I do it, or could wait for that to go in and re-use the functions)

Otherwise worked for me :)