Added logs to more steps :
- Panacus
- Squeeze
- SyRI
- Quast
- RagTag

Added threads to stats jobs

Added addition of SyRI figs in the final report if wanted

- Removed SyrI rule to get an All assembly figure ( will be replaced with a run of SyRI on chromosomes only instead of all assemblies)
- Renamed some rules for clarity
- Adding more elements to the final report

Offloading chromosome FASTA compression from clustering rule

This reverts commit 8b78a026.

Allowing retries for SyRI

Better RagTag fasta emptyness check

Not grouping samples anymore