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Vini2 / phables

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes
https://phables.readthedocs.io/
MIT License
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[Feature request] Handling mapping temporary files directory #45

Open pdec opened 3 months ago

pdec commented 3 months ago

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 commented 3 months ago

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 https://github.com/wwood/CoverM/issues/41. Hope this helps.

Thanks, Vijini