Scripts for routine analysis of clinical next generation sequencing (NGS) data at Viapath Genetics:
- demultiplex.py - Demultiplex Illumina NGS data using
bcl2fastq2(guide) - upload_and_setoff_workflows.py - Upload NGS data to DNANexus and trigger in-house workflows (guide)
The following modules are core dependencies:
- automate_demultiplex_config.py - Configuration for all automate demultiplex scripts
- decision_support_tool_inputs.py - Print inputs required by decision support tool upload applications on DNANexus
- adlogger.py - Logging module for automate demultipex script
Logfiles produced by automate demultiplex scripts are uploaded to the DNANexus project under PROJECT:/RUNFOLDER/Logfiles. See docs/ for each script's logfile details.
Alerts are sent to the #moka-alerts binfx slack channel. In the event of a critical failure an email is sent to the moka-guys mailing list.
Scripts are triggered by a cronjob on the linux workstation which can be updated using sudo crontab -e.
TBC