Automatically render coverage reports from Chanjo ouput
Project description
Chanjo Report
Automatically generate basic coverage reports from Chanjo SQL databases. This plugin installs as a subcommand ("report") to the Chanjo command line interface.
Usage
Chanjo Report supports a number of output formats: tabular, PDF, and HTML. To print a PDF coverage report for a group of samples "WGS-prep" do:
$ chanjo report --render pdf --group "WGS-prep" > ./coverage-report.pdf
Features
Supported output formats
Chanjo Reports multiple output formats:
- tabular: easily parsable and pipeable
- PDF: easily distributable (for humans)
- HTML: easily deliverable on the web
Supported languages (translations)
The coverage report (HTML/PDF) can be render is the following languages:
- English
- Swedish
Motivation
We are using the output from Chanjo at Clincal Genomics to report success of sequencing across the exome based on coverage. Our customers, clinicians mostly, are specifically interested in knowing to what degree their genes of interest are covered by sequencing along with some intuitive overall coverage metrics. They want the output in PDF format to file it in their system.
As a side effect of finding it easiest to convert HTML to PDF, Chanjo Report has a built in Flask server that can be used to render reports dynamically and even be plugged into other Flask servers as a Blueprint.
Installation
The latest version of Chanjo-report can be installed by cloning and installing the repository from Clinical Genomics github:
$ git clone https://github.com/Clinical-Genomics/chanjo-report.git
$ cd chanjo-report
$ pip install --editable .
Demo instance with Docker
To run a local demo with Docker, ensure you have a Docker engine running. If you do not have Docker set up, we can recommend Docker Desktop (https://www.docker.com/products/docker-desktop/).
Then use make with the repository Makefile to build and run:
make build
make setup
make report
Point your browser to http://127.0.0.1:5000 and find the demo samples.
Comprehensive instructions
We provide a Dockerfile to run the server in a container. To run a demo instance of the server with a pre-populated database consisting of a case with 3 samples, clone the repository using the following commands:
$ git clone https://github.com/Clinical-Genomics/chanjo-report.git
$ cd chanjo-report
Then you could make use of the services present in the Docker-compose file following these 3 steps:
-
Build the images
make build -
Launch chanjo to create a populate the database with demo data
make setup -
Launch the chanjo-report server
make report
A running instance of the server should now be available at the following url: http://localhost:5000/.
In order to generate a report containing all 3 demo samples, use the respective request args: http://localhost:5000/report?sample_id=sample1&sample_id=sample2&sample_id=sample3
Please be aware that if you are building and running the Dockerized version of chanjo-report, there might be issues on macOS if your processor is Apple silicon (or another ARM64 based architecture).
In order to build the chanjo-report image in the ARM64 architecture, you can set the environment variable DOCKER_DEFAULT_PLATFORM:
export DOCKER_DEFAULT_PLATFORM=linux/amd64
make build
make setup
make report
License
MIT. See the LICENSE file for more details.
Contributing
Anyone can help make this project better - read CONTRIBUTING to get started!
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