[Feature request] Handling mapping temporary files directory

[pdec]

Hey,

the temporary/partial bam files are created in the directory where I run phables rather than in the output directory.
Do you think it is possible to enhance that? *0001.bam, *0002.bam etc.

Isn't that handled by the coverm's --bam-file-cache-directory flag?

Cheers
Przemek

[Vini2]

Hi @pdec,

I think you can set the tmp directory for CoverM using the TMPDIR env variable. You can set it as follows.

TMPDIR=.

Got it from wwood/CoverM#41. Hope this helps.

Thanks,
Vijini

[Vini2]

Closing this issue. Please reopen if required.