I am just setting up the first nf-test for our pipeline, so I'm unsure about the compatiblity of things with our pipeline and the test suite.
I am getting an error when running an initial main.nf.test created with the nf-test generate command. The error is seen when running the test on a profile with an executor configuration to run processes the pipeline on Google Life Sciences (GLS).
> nf-test test --profile paths,gcp test/nf-test/main.nf.test
Executor `google-lifesciences` requires a Google Storage bucket to be specified as a working directory -- Add the option `-w gs://<your-bucket/path>` to your run command line or specify a workDir in your config file
Our GLS profile config looks something like this ($params defined in the main nextflow.config):
gcp {
workDir = "${params.work_path}/${params.full_tag}"
params.data_path = "gs://SOME_BUCKET"
...
...
process {
executor = 'google-lifesciences'
errorStrategy = { task.exitStatus in [0, 2, 10, 14] && task.attempt < 3 ? 'retry' : 'ignore' }
maxRetries = 3
}
}
I have tried re-defining the workDir in different ways, nf-test doesn't seem to pick them up. I haven't seen any good examples on using the tests/nextflow.config and none of what I've specified there appeared in the meta/params.json. Can someone point me to an example on the use of test-specific config file?
I've also tried running nf-test with another profile for GCP batch, correct me if I'm wrong, but it doesn't seem to be supported in the current version of nf-test.
Appreciate any help, thanks!
I am just setting up the first nf-test for our pipeline, so I'm unsure about the compatiblity of things with our pipeline and the test suite.
I am getting an error when running an initial
main.nf.testcreated with thenf-test generatecommand. The error is seen when running the test on a profile with an executor configuration to run processes the pipeline on Google Life Sciences (GLS).Our GLS profile config looks something like this (
$paramsdefined in the mainnextflow.config):I have tried re-defining the
workDirin different ways, nf-test doesn't seem to pick them up. I haven't seen any good examples on using thetests/nextflow.configand none of what I've specified there appeared in themeta/params.json. Can someone point me to an example on the use of test-specific config file?I've also tried running nf-test with another profile for GCP batch, correct me if I'm wrong, but it doesn't seem to be supported in the current version of nf-test.
Appreciate any help, thanks!