Automate collection of ONT QC metrics

[kedhammar]

For a new sequencing run, the PromethION script will now go through the instrument logs to find all previous pore counts recorded for the running flowcell, either from flow cell QC or sequencing MUX scans. This information will be dumped in the sequencing run directory (same as the run_path.txt).

TACA will then parse this information and append it to the CouchDB entry.

:)

[kedhammar]

TODO for deployment

• update the PromethION CRON job to 13 * * * * python3 ~/TACA-master/taca/nanopore/promethion_transfer.py --source /data/data-offload --dest /srv/ngi_data/sequencing/promethion --archive /data/nosync --minknow_logs /var/log/minknow/

• update AM1620

• manually touch pore_count_history.csv to any mid-transfer runs

[kedhammar]

Waiting on IT to remount Prom before deploying