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Ask user if they want to set NXF_TEMP #48

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georgiesamaha
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Closes #23

@jfy133
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jfy133 commented Feb 8, 2024

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?

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jfy133 commented Feb 8, 2024

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 :)

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Infrastructure config - new question: do you want to specify a specific scratch/TMPDIR space
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