Metadata-Version: 2.1
Name: janis-pipelines.pipelines
Version: 0.10.1
Summary: Bioinformatics tools for Janis; the Pipeline creation helper
Home-page: https://github.com/PMCC-BioinformaticsCore/janis-pipelines
Author: Michael Franklin
Author-email: michael.franklin@petermac.org
License: GNU
Description: # Janis - Example Pipelines
        
        [![PyPI version](https://badge.fury.io/py/janis-pipelines.pipelines.svg)](https://badge.fury.io/py/janis-pipelines.pipelines)
        
        This repository contains workflows written using [Janis](https://github.com/PMCC-BioinformaticsCore/janis).
        
        These workflows are installed by default, but are available on PIP with:
        ```bash
        pip3 install janis-pipelines.pipelines
        ```
        
        ## Documentation
        
        These pipelines are documented with run instructions here: https://janis.readthedocs.io/en/latest/pipelines/index.html
        
        ## More information
        
        These pipelines are made available through the entrypoint: `janis.extension=pipelines`.
        
        They can be imported in Python with the following:
        
        ```python
        from janis_pipelines import WGSGermlineGATK
        
        WGSGermlineGATK().translate("wdl")
        ```
        
        ## Pipelines
        
        **Whole genome sequencing (WGS) pipelines**:
        
        - [Germline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline/)
            - [Germline (GATK only)](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline_gatk)
        - [Somatic](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic/) 
            - [Somatic (GATK only)](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic_gatk)
        
        **Other**:
        
        - [Alignment](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/alignment/)
        
        
        ## Reference files:
        
        - Tested with `hg38` from [GCS: Broad Institute](https://console.cloud.google.com/storage/browser/genomics-public-data/references/hg38/v0/)
        
        
        ## WGS Germline pipeline
        
        > See the - [germline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline/)
        folder for more information, the workflow and CWL / WDL translations.
        
        The WGS germline pipeline takes a FASTQ pair, aligns, sorts, marks duplicates and calls variants
        across GATK4, Strelka and VarDict. These variants are combined and sorted at the end.
        
        These variants were validated against the [Genome in a Bottle](#) data sets to achieve:
        
        - Recall: 99.25%
        - Precision: 92.02%
        
        These results were identical across 3 research institutes (combination of Slurm / PBS / Torque) 
        and Google Cloud platform. The pipeline took approximately 27-30 hours to run at a 30x coverage,
        depending on the resource constraint.
        
        
        ## WGS Somatic pipeline for tumor-normal variant discovery
        
        > See the [somatic](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic/)
        folder for more information, the workflow and CWL / WDL translations.
        
        The WGS somatic pipeline takes normal and tumor FASTQ pairs, aligns, sorts and marks duplicates separately, and
         then performs tumor-normal variant discovery across GATK4, Strelka and VarDict (in somatic modes). These variants are combined and sorted at the end.
        
        This pipeline was run successfully across a similar set of research institutes (as germline) and the cloud,
        however these variants have not been validated yet.
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
