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.bammysample.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:
ToolInputto localise the index using a specific format (see: )ToolOutputto prepare your input for .
Documentation
Documentation is generated on Janis. To generate new documentation you will need to:
- Commit your changes here,
- Update the submodule pointer on Janis,
- Checkout Janis (recursively),
- Run the regenerate script
janis/docs/regeneratedocumentation.py, - Commit these changes and the documentation will autobuild on ReadTheDocs.
3 maintainers
Metadata
3 maintainers
Release files for janis-pipelines.bioinformatics 0.12.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| janis-pipelines.bioinformatics-0.12.2.tar.gz | 5.5 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| janis_pipelines.bioinformatics-0.12.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 11.2 MB
Release files / janis-pipelines.bioinformatics-0.12.2.tar.gz
| Download URL | janis-pipelines.bioinformatics-0.12.2.tar.gz |
|---|---|
| Size | 5.5 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.17
|
Release files / janis_pipelines.bioinformatics-0.12.2-py3-none-any.whl
| Download URL | janis_pipelines.bioinformatics-0.12.2-py3-none-any.whl |
|---|---|
| Size | 5.7 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.8.17
|
