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removes title from schema
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Geert van Geest committed Jul 31, 2024
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{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"title": "V-pipe configuration",
"description": "The V-pipe workflow can be customized through the configuration file `config.yaml` or `config.json` or, for backward compatibility with the [legacy INI-style format used in V-pipe v1.x/2.x](https://github.com/cbg-ethz/V-pipe/wiki/options), `vpipe.config`. This configuration file is a text file written using a basic structure composed of sections, properties and values. When using [YAML](https://yaml.org/spec/1.0/#id2564813) or [JSON](https://www.json.org/json-en.html) format use these languages associative array/dictionaries in two levels for sections and properties. When using the older [INI format](https://docs.python.org/3/library/configparser.html), sections are expected in squared brackets, and properties are followed by corresponding values.\n\nFurther more, it is possible to specify additional options on the command line using Snakemake's `--configfile` to pass additional YAML/JSON configuration files, and/or using Snakemake's `--config` to pass sections and properties in a [YAML Flow style](https://yaml.org/spec/1.2.0/#Flow)/JSON syntax.\n\nThe order of precedence is:\n_command line options (`--config`, `--configfile`)_ >> _default configuration file (`config/config.yaml` or `config.yaml`)_ >> _legacy configuration INI (`vpipe.config`)_ >> _Virus-specific base config (`virus_based_config`)_ >> _default values_\n\nExample: For instance, we suggest providing as input a tabular file specifying sample unique identifiers (e.g., patient identifiers), and dates for different sequencing runs related to the same patient. The name of this file (here, `samples.tsv`) can be provided by specifying the section as `input` and the property as `samples_file`, as follows in the example below.\n\nIn this document, we provide a comprehensive list of all user-configurable options stratified by sections.",
"examples": [{"input":{"samples_file":"samples.tsv"}}],
"properties": {
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