new config file not working

Yesterday I created the sandbox_vm.config file and merged it into master.

However, neither Simone nor me (running through Tower) can get the pipeline to run using this config.

Any ideas?

Yesterday I created the sandbox_vm.config file and merged it into master.

Dear @mdediegofuertes and @vrennie , I highly recommend that changes to the master not be merged before local testing otherwise, it becomes a time-sink for multiple people involved.

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I took a look at the code now #223, and the profile needs to be added in the nextflow.config files as shown below.

MAGMA/nextflow.config

Line 65 in bf355d0

biomina { includeConfig 'conf/biomina.config' }

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That being said, by including institution specific configuration in the pipeline, we are not moving in the right direction since it'll create a new dependency and when they have new VMs or something goes wrong with the IT or Azure setup, we have to accommodate the changes in pipeline config as well. They can always override the configuraiton using -c command.

Marking this issue as closed since this is not a bug, but rather a design choice.