Sentieon License file resolution breaks if not supplied

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

The Sentieon modules hard code some logic to fetch a secret and decide if it's a script or value.

In production, most users will set it to a DNS (sentieon-license-server.myorg.com:8990)

Move it into an optional path input for the process, it should work:

input:
// etc
path sentieon_license_file

script:
// etc
def sentieon_license_file ?: "export SENTIEON_LICENSE=${sentieon_license_file}"
// else SENTIEON_LICENSE must be set elsewhere, e.g. `env` configuration or `beforeScript`

Test users can supply a Sentieon License file as an input, while main users of Sentieon can supply the environment variable SENTIEON_LICENSE.

See https://github.com/nf-core/sarek/issues/2256

Command used and terminal output

n/a

Relevant files

n/a

System information

all

Start by locating the Sentieon modules and reading how they currently resolve the license secret. Check the related nf-core/sarek issue for context, then verify that a license-file input works while SENTIEON_LICENSE can still be supplied through environment configuration or beforeScript. Done means the hard-coded resolution no longer breaks DNS-based production use.