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Anselmo, Anthony
pipeline_monitor
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Tony Anselmo
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# pipeline_monitor
Scripts for Monitoring/Communicating Bioinformatic Pipeline Run Status (ex. Cromwell, Terra, ...)
Monitor & Communicate Cromwell Job Status
-------------
Description and Example Usage
-------------
python3 cromwell_monitor.py -j Demultiplex_IlluminaRun_Name \
http://34.72.194.35:8000 69f23a43-9f40-4152-ae60-609640fd1dbd
Note: The job name is optional.
Dependent on the following modules/scripts (in same folder):
command_run.py
message_slack.py
This code will allow the user to track when a cromwell job
(workflow id) has completed, whether successfully or not.
Cromwell returns 'Succeeded' for success and 'Failed' for failure
for final job status. The final job status will be emailed to
those addresses specified (hard-coded) in this script.
In addition, a Slack message will be sent via a webhook
to the channel specified (hard-coded) in the
message_slack.py script.
Information on Slack webhooks can be found here:
https://api.slack.com/messaging/webhooks
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