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API | ||
=== | ||
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``pgsc_calc`` is designed to be used in a terminal, but can also be launched | ||
programmatically on a Kubernetes cluster. To simplify this process, | ||
``pgsc_calc`` supports specifying target genomes and runtime parameters using | ||
JSON. | ||
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Specifying target genomes with JSON | ||
----------------------------------- | ||
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.. code-block:: json | ||
{ | ||
"target_genomes": [ | ||
{ | ||
"sample": "example", | ||
"vcf_path": "path.vcf.gz", | ||
"chrom": 22 | ||
} | ||
] | ||
} | ||
Target genomes are specified as a JSON array. Each element of the array must: | ||
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- Contain an experiment identifier ("``sample``"). If genomic data are split | ||
across multiple files (e.g. per chromosome), then this identifier must be the | ||
same across split files | ||
- Contain a path to a block gzipped Variant Call Format file ("``vcf_path``") | ||
- Specify which chromosome the variants come from ("``chrom``"). If the data are | ||
not split, then chrom can be null. | ||
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The target genome array must contain at least one item, and each item must be | ||
unique. | ||
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This JSON data must be saved to a file and used with the workflow parameter | ||
``--input`` in combination with ``--format json``. The file extension should end | ||
with ``.json``. | ||
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Specifying workflow parameters with JSON | ||
---------------------------------------- | ||
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JSON schema | ||
----------- |
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Input | ||
====== | ||
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You need some stuff | ||
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JSON | ||
---- | ||
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