Viloca automation

[mcarrara-bioinfo]

Added the logic to automate the run of VILOCA on the current deployed system.

Overview:

• The logic follows the same structure used to run vpipe
• Viloca is separated and autonomous from Vpipe

Steps:

• The status of the current run is checked
• If Viloca is not running, the system checks if it failed from the logs, to handle long run timeouts
  • if it failed, it unlocks the snakemake directory and restarts processing
• If viloca is finishing, archive the results in a dedicated archival dir on Euler, to make space for a new run
• If the Viloca has completed a run, the results are synced to BSSE
  • the sync currently archives only the most recent run
  • Help will be necessary to modify it to backup the entire archive and parallelize
• The system retrieves the latest batches analysed by vpipe and viloca
• if they differ, the system assumes there is a new batch to run viloca on
• The system builds the samplelist from the samples files following the viloca requirements
• the samplelist is pushed to the work-viloca folder on euler
• if the push is successful, viloca is started

Currently viloca fails to run due to a problem in the latest version of the rules. While this is being solved, I suggest to deploy the changes with the Viloca processing disabled.

Support for deployment may be necessary as both the local and remote repository currently in production have several uncommitted changes compared to the master branch