I am using nf-core/sarek for a while and started to try raredisease now! But when I´ve run for the first time I received the error below....Anyone can help me? Thanks a lot!

params.variant_consequences_snv not set.
params.variant_consequences_sv not set.
params.ploidy_model not set.
params.gcnvcaller_model not set.
params.readcount_intervals not set.
params.mobile_element_references not set.
params.mobile_element_svdb_annotations not set.

my command was:

nextflow run nf-core/raredisease --input /home/zvasconcelos/data/raredisease_run/samplesheet_raredisease.csv -profile azurebatch -c /home/zvasconcelos/azure.config.brazil.supernew.big.raredisease -w '<az://genomas-raros/work>' --outdir '<az://genomas-raros/results/>'

Can you run the test-profile for nf-core/raredisease?

Yes!

Hello Zilton, I apologize for the delay in my response; I'm still catching up on my backlog after my vacation. 😅 I agree that the error message could use clearer wording. I will work on improving that in our codebase soon. Essentially, the message indicates that some parts of the pipeline you are trying to run are missing necessary inputs. From your message, I noticed that the following parameters are set to true: "skip_snv_annotation," "skip_sv_annotation," "skip_germlinecnvcaller," "skip_me_calling," and "skip_me_annotation." Setting them to false should make this error go away.