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Package file

Run Package

For repeated jobs, using a .yml file with job definition is handy.

For example, consider the following ov run job:

ov run input.vcf -a clinvar cosmic dbsnp -t csv

The configuration of this job can be written in run.yml file as follows:

- clinvar
- cosmic
- dbsnp
report_types: csv

Then, this file can be used as follows.

ov run input.vcf --package run.yml

which will work in the same way as the first ov run command.

Below are the correspondence between ov run options and the fields in package .yml files.

ov run option type package file (.yml) option
-a list annotators
-p list postaggregators
-t list report_types
-n string run_name
-d string output_dir
--clean bool clean
--genome string genome
-i string input_format
--startat string startat
--endat string endat
--skip list skip
--keep-temp bool keep_temp
--mp integer mp
--primary-transcript string primary_transcript
--module-options dict module_options
--vcf2vcf bool vcf2vcf
--logtofile bool logtofile
--ignore-sample bool ignore_sample