Closed adamkoletis closed 2 years ago
I believe you need to use, --medaka_model r941_min_hac_variant_g507
.
I apologise that this is not more clear, we rely on the nf-core project to provide the option parsing and CLI help messages and I've just noticed that this doesn't generate a list of the valid option values.
How we can access the model list names?
They are listed here: https://github.com/epi2me-labs/wf-artic/blob/master/nextflow_schema.json#L114
Again, apologies that they are not available with nextflow run ... --help
. I'll talk to the nf-core people about that.
Thanks this is clear and the model is now working - would be great to have this somewhere more obvious and easily accessible.
Hi, may I ask is the _variant family performs same as the other models?
The _variant
family is the set which is appropriate for the purposes of calling variants from reads aligned to a reference sequence. The non-_variant
models are used for polishing draft assemblies and are not intended for calling variants. This is why wf-artic restricts the choice to the _variant
family.
oic. Thanks a lot!
By running this command
appears issue
How we can resolve this please?