Watch a path for new illumina runs to arrive. When they arrive, parse the SampleSheet.csv file for the run and publish the details to a tcp port.
This service uses ZeroMQ CURVE authentication, which requires a public/private key pair.
One can use generate_certificates.py from the pyzmq examples security repository to create these keys.
usage: publish_illumina_runs.py [-h] [--port PORT] [--path PATH]
[--heartbeat_interval HEARTBEAT_INTERVAL]
[--print_heartbeat]
[--public_key PUBLIC_KEY] [--private_key PRIVATE_KEY]
optional arguments:
-h, --help show this help message and exit
--port PORT
--path PATH
--heartbeat_interval HEARTBEAT_INTERVAL
--print_heartbeat
--public_key PUBLIC_KEY
--private_key PRIVATE_KEY
Note: multiple paths can be watched simultaneously. eg:
publish_illumina_runs.py --path /path/to/sequencer-01 --path /path/to/sequencer-02
A simple demo subscriber script is included. It simply prints messages from the illumina_runs topic to stdout.
usage: demo_subscriber.py [-h] [--port PORT]
[--public_key PUBLIC_KEY] [--private_key PRIVATE_KEY]
optional arguments:
-h, --help show this help message and exit
--port PORT
--public_key PUBLIC_KEY
--private_key PRIVATE_KEY
Messages are published to the illumina_runs topic. There are currently four message types
{
"timestamp": "2020-10-01T17:23:56.597547",
"event": "heartbeat"
}{
"timestamp": "2020-10-05T15:42:09.605165",
"event": "run_directory_created",
"path": "/path/to/201001_M00325_0210_000000000-A5B31",
"run_id": "201001_M00325_0210_000000000-A5B31",
"parsed_data": {
"run_date": "2020-10-01",
"instrument_id": "M00325",
"run_number": "0210",
"flowcell_id": "000000000-A5B31",
}
}{
"timestamp": "2020-10-05T15:42:09.855106",
"event": "sample_sheet_created",
"path": "/path/to/201001_M00325_0210_000000000-A5B31/SampleSheet.csv",
"run_id": "201001_M00325_0210_000000000-A5B31",
"parsed_data": {
"header": {
"experiment_name": "Truly Insightful Experiment",
"instrument_type": "MiSeq",
"workflow": "GenerateFASTQ",
"investigator_name": "Dr. Sequencer",
"chemistry": "Amplicon"
},
"reads": [
251,
251
],
"settings": {
"reverse_complement": 0,
"adapter": ""
},
"data": [
{
"sample_id": "S1",
"sample_name": "Sample-01",
"sample_plate": "",
"sample_well": "",
"i7_index_id": "H714",
"index": "GCTCATGA",
"i5_index_id": "H506",
"index2": "ACTGCATA",
"sample_project": "",
"description": ""
},
...
]
}
}{
"timestamp": "2020-10-05T15:42:10.001029",
"event": "run_completion_status_created",
"path": "/path/to/201001_M00325_0210_000000000-A5B31/RunCompletionStatus.xml",
"run_id": "201001_M00325_0210_000000000-A5B31",
"parsed_data": {
"run_id": "201001_M00325_0210_000000000-A5B31",
"completion_status": "SuccessfullyCompleted",
"step_completed": 23,
"cycle_completed": 518,
"error_description": "None"
}
}