Unhelpful error message in nf-core download when container registry is not defined or is wrong about tools HOT 2 OPEN

In case anyone else is playing along with what I'm attempting to do, i.e. deploying non nf-core pipelines using download. I had to cut-and-paste the following nf-core stuff into the config to make it work:

params {
    // Config options
    custom_config_version      = 'master'
    custom_config_base         = "${projectDir}/../configs/"
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null
    config_profile_name        = null
}
// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
singularity.cacheDir = "${projectDir}/../singularity-images/"

from tools.

I could gather after carefully reading the commandline output that it tried to download the images from quay.io when in reality the images are hosted on docker.io.

Since nf-core images are primarily hosted on quay.io, I believe it is a reasonable default, if no explicit -l / --container-library parameter has been specified. The only alternative would be to make this argument mandatory without a default?

The error message was not helpful in immediately identifying this as it only stated that it "failed for unclear reasons."

Admittedly, this is not ideal. Since nf-core download only operates on the stderr output of singularity pull to assess the cause of an error, it is somewhat limited. The registries have different error messages in the response bodies of the request, and it is difficult to keep the regexes/keywords appropriately in sync despite a corresponding test. Please feel free to submit a PR suggesting an appropriate change to the ContainerError class to make it work in that case.

The better solution would be to make a separate request to the URI prior to trying singularity pull and utilize the HTTP status codes rather than bits of the response body text. Again, if you feel like implementing this, a PR is more than welcome.

from tools.