These are chat archives for nextflow-io/nextflow
I'm currently having problem configuring the K8s exectutor while running nextflow version 19.04.0
My config for it is defined as such:
storageClaimName = 'pvc-nfs'
storageMountPath = '/mnt/abc'
namespace = 'devel'
projectDir = '/mnt/abc/workflow/project'
The problem is that the executor seems to ignore the project dir, ie it doesn't download the project to this location, but instead uses the /.nextflow/assets directory within the pod that's running the nextflow executable.
This results in none of the processes executing having access to files included within the repository (for example the /bin directory).
Am I missing some crucial config information or is this a bug? :)
Ólafur Haukur Flygenring
then scripts being run with the k8 executor via the run command won't have access to files included in the script repository
The documentation on projectDir suggests that for the k8s executor the projectDir config entry is doing similar things to NXF_ASSETS and makes no mentions of it only working when using the kuberun command :)
"Defines the path where Nextflow projects are downloaded. This must be a path in a shared K8s persistent volume "
nextflow configin the launch path
nextflow.configfile in the launch directory?
singularity pull ...? The reason is that we need to dynamically set some singularity authentication variables.
process.beforeScriptjust with the difference that it is executed before the pipeline starts rather than before a process starts