Options -m and -v not recognised

[gkapatai]

Running this command:

phenix.py prepare_reference -v gatk -m bowtie2 -r reference.fasta

returned this error: phenix.py: error: unrecognized arguments: -v gatk -m bowtie2

When command changed to:

prepare_reference --variant gatk --mapper bowtie2 -r reference.fasta

it worked fine.

[alexjironkin]

Where does it mention to run prepare_reference with -v and -m options?

[ulfschaefer]

As per the help and the documentation the shortened version of the parameters are not available for these options.

usage: phenix.py prepare_reference [-h] --reference REFERENCE
[--mapper MAPPER] [--variant VARIANT]

Prepare reference for SNP pipeline by generating required aux files.

optional arguments:
-h, --help show this help message and exit
--reference REFERENCE, -r REFERENCE
Path to reference file to prepare.
--mapper MAPPER Available mappers: ['bwa', 'bowtie2']
--variant VARIANT Available variants: ['mpileup', 'gatk']