My organisation runs nf-core and in house pipelines using the Seqera platform - and have been doing this successfully for some time using Azure.
Running a pipeline which has been successful in the past I am getting a minimal error on the platform which in the past has been caused by something like a parameter validation error. -
The workflow execution failed to start. Exit status: 1
When I access the batch pool and observe the node logs, however, it looks like the nextflow run is not picking up any of the parameters I have submitted via the Seqera platform. This results in a default set being run and a parameter validation error:
Jul-03 10:11:08.935 [main] DEBUG nextflow.Session - Session aborted -- Cause: e[0;31mThe following invalid input values have been detected:
* Missing required parameter: --input
* Missing required parameter: --outdir
I have tried inputing the parameter values myself, and uploading a json from previously successful runs - but both cause the same error. I have tried a number of different compute environments which were all working last week.
Any help with this would be great.