{ "info": { "author": "Michael Franklin", "author_email": "michael.franklin@petermac.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "# Janis - Example Pipelines\n\n[![PyPI version](https://badge.fury.io/py/janis-pipelines.pipelines.svg)](https://badge.fury.io/py/janis-pipelines.pipelines)\n\nThis repository contains workflows written using [Janis](https://github.com/PMCC-BioinformaticsCore/janis).\n\nIt can be installed through PIP with:\n\n```bash\npip3 install janis-pipelines.pipelines\n```\n\nThis allows Janis to find these installed pipelines from the CLI (through entrypoint: `janis.extension=pipelines`) and means they can be imported from any Python file.\n\n```python\nfrom janis_pipelines import WGSGermlineGATK\n\nWGSGermlineGATK().translate(\"wdl\")\n```\n\n## Pipelines\n\n**Whole genome sequencing (WGS) pipelines**:\n\n- [Germline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline/)\n - [Germline (GATK only)](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline_gatk)\n- [Somatic](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic/) \n - [Somatic (GATK only)](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic_gatk)\n\n**Other**:\n\n- [Alignment](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/alignment/)\n\n## Quickstart\n\nTo use these pipelines, you will need to have Janis installed:\n\n```bash\npip3 install janis-pipelines\n```\n\nThen you can run the pipeline through Janis:\n\n```bash\nWORKFLOW=\"https://raw.githubusercontent.com/PMCC-BioinformaticsCore/janis-pipelines/master/workflows/alignment/alignment.py\"\n\n# Generate inputs file\njanis inputs WGSGermlineGATK > myinps.yml\n\n# Run workflow\njanis run --inputs myinps.yml WGSGermlineGATK\n```\n\n\n## WGS Germline pipeline\n\n> See the - [germline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_germline/)\nfolder for more information, the workflow and CWL / WDL translations.\n\nThe WGS germline pipeline takes a FASTQ pair, aligns, sorts, marks duplicates and calls variants\nacross GATK4, Strelka and VarDict. These variants are combined and sorted at the end.\n\nThese variants were validated against the [Genome in a Bottle](#) data sets to achieve:\n\n- Recall: 99.25%\n- Precision: 92.02%\n\nThese results were identical across 3 research institutes (combination of Slurm / PBS / Torque) \nand Google Cloud platform. The pipeline took approximately 27-30 hours to run at a 30x coverage,\ndepending on the resource constraint.\n\n\n## WGS Somatic pipeline for tumor-normal variant discovery\n\n> See the [somatic](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines/tree/master/workflows/wgs_somatic/)\nfolder for more information, the workflow and CWL / WDL translations.\n\nThe WGS somatic pipeline takes normal and tumor FASTQ pairs, aligns, sorts and marks duplicates separately, and\n then performs tumor-normal variant discovery across GATK4, Strelka and VarDict (in somatic modes). 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