Running test: "Cannot get property 'args' on null object"

[AlexWeinreb]

Description of the bug

When running the test pipeline, I get the error:

Cannot get property 'args' on null object

This can be traced back to line 116 of main.nf:

umitools_whitelist_options.args  += params.umitools_bc_pattern     ? " --bc-pattern='${params.umitools_bc_pattern}'"       : ''

After some playing around, I think it's because test.config defines a params.modules which overwrites the list defined in modules.config.

The problem disappears when commenting out lines 52-57 of test.config, which were introduced in commit e02ff48.

(although I then run into another Amazon S3 problem, opening separate issue)

Steps to reproduce

nextflow run salzmanlab/nf-sicilian -profile test -r dev

in a configured conda environment.

System

• Hardware: HPC
• Executor: SLURM

Nextflow Installation

• Version: 22.04.5.5708