janis-pipelines.bioinformatics 0.12.2

Bioinformatics tools for Janis; the Pipeline creation helper

Janis - Bioinformatics Toolbox

This repository is the bioinformatics toolbox for Janis. It contains tools and data types directly related to the bioinformatics field.

You can see a full list of tools in the documentation.

Data types

The data types are a way of encapsulating information about the file (including secondary files), and it allows clarity when connecting inputs and steps together. Sometimes bioinformatics data types have associated files (like an indexed bam, or a fasta with various indexes); when you use these types, Janis will bundle your files together to be transported around.

Indexed Bam

Further information: Secondary / Accessory files

Janis is opinionated about the .bai index for a Bam. Specifically we use the pattern:

• mysample.bam
• mysample.bam.bai

If your tool expects, or creates a file in the other common format (.bam and .bai), you can use the secondaries_present_as attribute on a:

• ToolInput to localise the index using a specific format (see: )
• ToolOutput to prepare your input for .

Documentation

Documentation is generated on Janis. To generate new documentation you will need to:

1. Commit your changes here,
2. Update the submodule pointer on Janis,
3. Checkout Janis (recursively),
4. Run the regenerate script janis/docs/regeneratedocumentation.py,
5. Commit these changes and the documentation will autobuild on ReadTheDocs.