Bug: config tmp folder is ignored during rRNA filtering
The given tmp folder path (i.e. the one specified in the snakemake
config file) seems to be ignored by mktemp
in the rRNA filtering rule: https://git-r3lab.uni.lu/IMP/imp3/-/blob/master/workflow/rules/Preprocessing/rna.filtering.smk#L10.
Though the CMD for mktemp
looks correct during the execution, the path being used is /tmp
which might cause issues for big FASTQ files.
As long as this issues is not resolved, the problem can be avoided by setting the shell variable TMPDIR
when running snakemake
:
TMPDIR="path/to/tmp/" snakemake ...