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    "info": {
        "author": "Michael Franklin",
        "author_email": "michael.franklin@petermac.org",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Developers",
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            "Topic :: Scientific/Engineering"
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        "description": "# Welcome to Janis-Assistant\n\n[![Build Status](https://travis-ci.org/PMCC-BioinformaticsCore/janis-assistant.svg?branch=master)](https://travis-ci.org/PMCC-BioinformaticsCore/janis-assistant)\n[![PyPI version](https://badge.fury.io/py/janis-pipelines.runner.svg)](https://badge.fury.io/py/janis-pipelines.runner)\n\n[Janis](https://github.com/PMCC-BioinformaticsCore/janis) is a workflow assistant designed \nto make the process of building and running workflows easier. \n\nMore specifically:\n\n- Janis core is a framework for specifying workflows, that can be transpiled to CWL and WDL.\n- Janis assistant runs manages an engine to these workflows and collects the results. \n\n## Quick start\n\n```bash\npip3 install janis-pipelines\n```\n\n### CWLTool\n\nYou can run a workflow in CWLTool with the following command line: \n```bash\njanis run --engine cwltool hello\n```\n\nTo use CWLTool, you must have CWLTool in your path with either Docker or Node, see [Engine support](https://janis.readthedocs.io/en/latest/references/engines.html)\nfor more information.\n\n### Cromwell\n\nCromwell is the default engine, and can be ran with:\n```bash\njanis run --engine cromwell hello\n```\n\nTo use Cromwell, you must have Java 1.8 available. See [Engine support](https://janis.readthedocs.io/en/latest/references/engines.html#id2)\nfor more information.\n\n## CLI options:\n\n- `run` - Run a janis workflow (see the run parameters below)\n- `watch` - Watch an existing execution (folder or workflow ID)\n- `abort` - Issue an abort request to an existing execution\n- `inputs` - Generate an inputs file for a workflow\n- `translate` - Translate a workflow into CWL / WDL\n- `metadata` - Get the available metadata on an execution\n- `version` - Print the version of `janis` submodules.\n- `spider` - Print documentation for a tool (allows to trace problems with the Janistoolbox)\n\n### `run`\n\nYou can run a workflow with the `run` method, here's an example to run the hello world example:\n\n```bash\njanis run hello\n```\n\nView the help guide \n\n```\n# $ janis run -h\n\npositional arguments:\n  workflow              Run the workflow defined in this file or available\n                        within the toolbox\n  extra_inputs\n\noptional arguments:\n  -h, --help            show this help message and exit\n  -i INPUTS, --inputs INPUTS\n                        YAML or JSON inputs file to provide values for the\n                        workflow (can specify multiple times)\n  -o OUTPUT_DIR, --output-dir OUTPUT_DIR\n                        This directory to copy outputs to. By default\n                        intermediate results are within a janis/execution\n                        subfolder (unless overriden by a template)\n  -B, --background      Run the workflow engine in the background (or submit\n                        to a cluster if your template supports it)\n  --progress            Show the progress screen if running in the background\n  --keep-intermediate-files\n                        Do not remove execution directory on successful\n                        complete\n  --skip-file-check     Skip checking if files exist before the start of a\n                        workflow.\n  --allow-empty-container\n                        Some tools you use may not include a container, this\n                        would usually (and intentionally) cause an error.\n                        Including this flag will disable this check, and empty\n                        containers can be used.\n  --development         Apply common settings (--keep-execution-dir + --mysql)\n                        to support incremental development of a pipeline\n\ninput manipulation:\n  -r RECIPE, --recipe RECIPE\n                        Use a provided recipe from a provided template\n  --max-cores MAX_CORES\n                        maximum number of cores to use when generating\n                        resource overrides\n  --max-memory MAX_MEMORY\n                        maximum GB of memory to use when generating resource\n                        overrides\n\nhints:\n  --hint-captureType {targeted,exome,chromosome,30x,90x,300x}\n  --hint-engine {cromwell}\n\nworkflow collection arguments:\n  --toolbox            Skip looking through the search path, and only look in\n                        the toolbox\n  -n NAME, --name NAME  If you have multiple workflows in your file, you may\n                        want to help Janis out to select the right workflow to\n                        run\n  --no-cache            Force re-download of workflow if remote\n\nengine arguments:\n  --engine {cwltool,cromwell}\n                        Choose an engine to start\n  --cromwell-url CROMWELL_URL\n                        Location to Cromwell\n\nfilescheme arguments:\n  -f {local,ssh}, --filescheme {local,ssh}\n                        Choose the filescheme required to retrieve the output\n                        files where your engine is located. By selecting SSH,\n                        Janis will SCP the files using the --filescheme-ssh-\n                        binding SSH shortcut.\n  --filescheme-ssh-binding FILESCHEME_SSH_BINDING\n                        Only valid if you've selected the ssh filescheme. (eg:\n                        scp cluster:/path/to/output local/output/dir)\n\nvalidation arguments:\n  --validation-reference VALIDATION_REFERENCE\n                        reference file for validation\n  --validation-truth-vcf VALIDATION_TRUTH_VCF\n                        truthVCF for validation\n  --validation-intervals VALIDATION_INTERVALS\n                        intervals to validate between\n  --validation-fields VALIDATION_FIELDS [VALIDATION_FIELDS ...]\n                        outputs from the workflow to validate\n\nbeta features:\n  --mysql               BETA: Run MySQL for persistence with Cromwell\n```\n\n## Configuration\n\nIt's possible to configure a number of attributes of `janis_assistant`. \nYou can provide a YAML configuration file in two ways:\n\n- CLI: `--config /path/to/config.yml`\n- Environment variable `JANIS_CONFIGPATH=/path/to/config.yml`\n- Default: `$(HOME)/.janis/janis.conf` - will additionally look for a config here.\n\n> Configurations aren't currently cascaded, but the intention is they will.\n\n### Options\n\nDefaults: [`janis_assistant/management/configuration.py`](https://github.com/PMCC-BioinformaticsCore/janis-assistant/blob/master/janis_assistant/management/configuration.py#L68)\n\n- Config / DB directory: `configDir: /path/to/configir/`\n    - Second priority to environment variable: `JANIS_CONFIGDIR`\n    - Default: `(HOME)/.janis/`\n    - Database: `{configDir}/janis.db` - Janis global database\n\n- Execution directory: `executionDir`\n    - Second priority to environment variable: `JANIS_EXCECUTIONDIR`\n    - Default: `(HOME)/janis/execution/`\n\n- Search paths: `searchPaths`\n    - Will additionally add from environment variable: `JANIS_SEARCHPATH`\n    - Default: `(HOME)/janis/`\n\n\n## Engines\n\nThere are currently 2 engines that `janis_assistant` supports:\n\n1. CWLTool\n2. Cromwell\n\n### CWLTool (default)\n\nDue to the way CWLTool provides metadata, support for CWLTool is very basic, and limited to submitting \nworkflows and linking the outputs. Janis can manage CWLTool in the background, except if CWLTool is \nterminated (through some transient cluster error), Janis is unable to restart it.\n\n\n### Cromwell\n\nCromwell can be run in two modes:\n\n1. Connect to an existing instance (well supported) - include the `--cromwell-url` argument with the port to \n    allow the Janis assistant to correctly connect to this instance.\n\n2. Run and manage it's own instance. When the task is started, the `process_id` of the started Cromwell instance\n    is stored in the `taskdb`, when the task finishes execution, Janis stops this Cromwell instance. Janis\n    can manage a MySQL (in fact MariaDB) instance with the `--mysql` flag for durability and to reduce memory overhead.\n\nBoth of these options provide reporting and progress tracking due to Cromwell's extensive metadata endpoint. The TaskID\n(6 hex characters) is included as a label on the workflow.\n\n```bash\njanis watch $tid\n``` \n\nA screenshot of the running the example [whole genome germline pipeline](https://github.com/PMCC-BioinformaticsCore/janis-examplepipelines)\n (for a targeted sample) can be found below. (All engines can support this through a generalised metadata semantic (`TaskMetadata`),\n Neither CWLTool or Toil support much polling of metadata).\n\n> ![Screenshot of janis progress screen](resources/metadata-progress.png)\n\nExtra Cromwell comments:\n\n- The TaskID is bound as a label on GCP instances (as `wid`, allowing you to query this information).\n- Janis uses the development spec of WDL, requiring Cromwell-42 or higher.\n- If asking Janis to start its own Cromwell instance, it requires the jar to be exported as `$cromwelljar`.\n\n\n### Databases\n\n> This feature requires better documentation in the primary Janis documentation.\n\nSome features of Cromwell require a database to use: call-caching, resumability for cluster failures and so on.\n\nPreviously, this has been managed through automatically spinning up a mysql instance with Docker / Singularity, however this has been unstable. Now, as Cromwell supports a [file-based database](https://cromwell.readthedocs.io/en/stable/Configuring/#database), this is now the default.\n\n- No options -> file-based DB\n- `--no-database` -> No database is ran\n- `--mysql` -> Automatically provision and manage a mysql server (unchanged)\n- Configure an existing \n\nCall caching has been enabled by default using the `file` based method, we strongly recommend downloading Cromwell >50 and using `fingerprint`, see [call caching documentation](https://janis.readthedocs.io/en/latest/references/callcaching.html) for more information.\n\nWARNING: `fingerprint` will become the default once Cromwell 50 has been released. This might break if you're using older versions of Cromwell.\n\n\n### Filesystem\n\nThere is a weak concept of a filesystem for where your workflow is executed. This tool is really only developed\nfor using the `LocalFileSystem`.\n\nSupported filesystems:\n\n- LocalFileScheme\n- SSHFileScheme (`identifier`, `connectionstring`) - I'd recommend creating an \n    [SSH shortcut](https://scotch.io/tutorials/how-to-create-an-ssh-shortcut) to avoid persisting personal details in\n    database. Janis uses the connection string like so: `scp connectionstring:/path/to/output /local/persist/path`\n\n\n## Databases\n\nJanis stores a global SQLite database at `{configDir}/janis.db` of environments and task pointers \n(default: `~/.janis/janis.db`). When a task is started, a database and workflow files are copied \nto your specified output directory.\n\n\n\n",
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