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janis-workshops

This repository contains workshops for the Janis pipeline framework.

  1. Introduction to Janis
  2. Building a basic bioinformatics workflow
  3. Wrapping a new CommandTool
  4. Advanced workflow concepts

You can find more documentation about Janis here: https://janis.readthedocs.io/en/latest/

Quickstart

You can install Janis using pip:

pip3 install janis-pipelines[bioinformatics]

Workshop material

These guides and notes are designed to assist a participant attending a workshop and can't be seen as a replacement to a physical session. The guides and data (where available) are published under GPL3.

Every piece of data should be referenced, please raise an issue if that's not the case.

Data

The BRCA1 samples are sourced from the SAMN03492678 study of NA12878 of the Genome in a Bottle project:

  • BRCA1_30X: gene BRCA1 from the WGS_30X:
  • Calculated coverage: 33.6X
  • Location: 17:43044295-43125483 (from NCBI)
  • Extract reads in 17:43044045-43125733 (+- 250bp)

Reference data

Processing and preprocessing of the NA12878 data used a modified HG38 reference genome with renamed contigs.