test config igenome configurations are wrong

[kubranarci]

Description of the bug

Hello,

Running test profile results with:

Genome 'GRCh37' not found in any config files provided to the pipeline. Currently, the available genome keys are: hg38, hg19

error.

I checked the config file and realized --ignore_igenomes is turned to be true which has to be on if user wants to use of --genome parameter.

Encountering this error made me to go through github actions since yesterday there was a new release published. I realized CI checks only includes runs with -stub checks. -Stub runs are useful to technically check the pipelines but CI checks should involve real runs as well to be able to catch up with these kind of errors.

Best,

Command used and terminal output

Relevant files

No response

System information

No response

[kubranarci]

btw, I guess the need to turn off igenomes is because the profile needs to use custom fasta files. Yet, genome parameter is also being used with VEP which cannot be closed. I think the best solution to this to make another genome parameter for VEP.