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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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medaka_model is not a valid enum value #18

Closed adamkoletis closed 2 years ago

adamkoletis commented 2 years ago

By running this command 

nextflow run epi2me-labs/wf-artic -profile standard -w OUTPUT_DIRECTORY/work --samples /sample_sheet --fastq FASTQ_FOLDER --out_dir OUTPUT_DIRECTORY --scheme_version V1200 --medaka_model r941_min_hac_g507

appears issue

How we can resolve this please?

cjw85 commented 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.

adamkoletis commented 2 years ago

How we can access the model list names?

cjw85 commented 2 years ago

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.

LianaKafetzopoulou commented 2 years ago

Thanks this is clear and the model is now working - would be great to have this somewhere more obvious and easily accessible.

llk578496 commented 2 years ago

Hi, may I ask is the _variant family performs same as the other models?

cjw85 commented 2 years ago

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.

llk578496 commented 2 years ago

oic. Thanks a lot!