Speedup FRASER couting on Cluster

[mumichae]

Copy BAM files to local resources.tmpdir for faster processing. This would probably require Snakemake>=6.0

[c-mertes]

Hey, two points:

1. is the temp folder run specific? Otherwise we could remove the file if concurrent processes are accessing the files. E.g. multiple datasets will run it multiple times.

2. this is really infrastructure dependent and could degrade others performance. Did you do benchmarks on the efficiency?

[mumichae]

Sorry for the late reply.

1. The tmp folder is ID specific, so I would assume it is run specific, as Snakemake shouldn't be running two IDs twice.
2. I did not benchmark the efficiency, it's just something I used to speed up the aberrant splicing module. Even if with lower file latency, I don't think it would hurt, but if you find this modification unneccessary, I can also close this issue.