Package.rst

Package

Package is a module which defines module installation and job parameters. For example, if you use the below process often:

• Install ClinVar and COSMIC modules.
• Annotate with ClinVar and COSMIC modules.
• Collect missense mutations only.
• Make VCF-format reports.

This process can be defined in a package module and you can tell OpenCRAVAT to do exactly the same process by giving the package's name to OpenCRAVAT as an option.

Making a Package

A package is a regular OpenCRAVAT module. In your OpenCRAVAT modules directory (you can find it with oc config md), make packages if it does not exist, and then create a package directory with a package name of your choice (should be unique among all modules) under the packages directory (for example, mypackage). Then, create a .py and a .yml file with the package name. For example,

OpenCRAVAT modules directory/
|
+- packages/
   |
   +- mypackage/
      |
      +- mypackage.py
         mypackage.yml

The .py file can be empty and is not used by OpenCRAVAT, but it needs to exist for administrative purposes. The .yml file defines the dependency and process of the package. An example of mypackage.yml is below.

title: Allele Frequency Package
description: Population allele frequency package with 1000 Genomes, ESP6500, gnomdAD, and gnomAD3
type: package
version: 0.0.1
# Modules for this package
requires:
- thousandgenomes
- esp6500
- gnomad
- gnomad3
# oc run and oc report settings
run:
    # Annotators
    annotators:
    - thousandgenomes - esp6500
    - gnomad
    - gnomad3
    # Reports
    reports:
    - vcf
    # Filters
    filtersql: >
      (
        (v.base__so = 'IND')
        or
        (v.base__so = 'INI')
        or
        (v.base__so = 'MIS')
      )
      and
      (g.base__hugo = 'BRAF')
    includesample:
    - sample1
    excludesample:
    - sample2

Yon can use a package as an option to oc run and oc report.

Using a Package

Use --package option with oc run or oc report command to apply a package's settings to run a job or create a report. For example,

oc run input --packge mypackage

This will run thousandgenomes, esp6500, gnomad, and gnomad3 annotator modules on input and create a VCF-format output file only with the variants that are in the gene BRAF, produce either inframe insertion, inframe deletion, or missense protein sequence consequence, exist in sample1, and do not exist in sample2.

oc report input.sqlite --package mypackage

This will create a VCF-format output file only with the variants, among the variants in input.sqlite, that are in the gene BRAF, produce either inframe insertion, inframe deletion, or missense protein sequence consequence, exist in sample1, and do not exist in sample2.