MAGMA (Maximum Accessible Genome for Mtb Analysis) is a pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research.
- Fine-grained control over resource allocation (CPU/Memory/Storage)
- Reliance of bioconda for installing packages for reproducibility
- Ease of use on a range of infrastructure (cloud/on-prem HPC clusters/ servers (or local machines))
- Resumability for failed processes
- Centralized locations for specifying analysis parameters and hardware requirements
- MAGMA parameters (
default_parameters.config) - Hardware requirements (
conf/standard.config) - Execution (software) requirements (
conf/docker.configorconf/conda.config)
- MAGMA parameters (
- An (optional) GVCF reference dataset for ~600 samples is provided for augmenting smaller datasets
Note Downloading the reference EXIT_RIF GVCF files from FIXME
For the tutorials(./docs/tutorials.md) and presentations please refer the docs folder.
git: The version control in the pipeline.Java-11orJava-17(preferred)
NOTE: The java version should NOT be an internal jdk release! You can check the release via java -version
- Download Nextflow
$ curl -s https://get.nextflow.io | bash- Make Nextflow executable
$ chmod +x nextflow- Add
nextflowto yourpath(for example/usr/local/bin/)
$ mv nextflow /usr/local/bin
- Sanity check for
nextflowinstallation
$ nextflow info
Version: 22.04.5 build 5708
Created: 15-07-2022 16:09 UTC (18:09 SAST)
System: Mac OS X 10.15.6
Runtime: Groovy 3.0.10 on OpenJDK 64-Bit Server VM 11.0.9.1+1-LTS
Encoding: UTF-8 (UTF-8)
- Local Conda environments for MAGMA
- Docker based execution for MAGMA
- HPC based execution for MAGMA
- Cloud batch (AWS/Google/Azure) based execution for MAGMA
The MAGMA pipeline paper has been submitted.
The XBS variant calling core was published here: https://doi.org/10.1099%2Fmgen.0.000689
TODO: Update this section and add a citation.cff file
Contributions are warmly accepted!
Please refer the GPL 3.0 LICENSE file.