draft docs

docs/api.rst

@@ -0,0 +1,45 @@
+API
+===
+
+``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.
+
+
+Specifying target genomes with JSON
+-----------------------------------
+
+.. 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:
+
+- 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.
+
+The target genome array must contain at least one item, and each item must be
+unique.
+
+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``.
+
+Specifying workflow parameters with JSON
+----------------------------------------
+
+JSON schema
+-----------

docs/conf.py

@@ -17,9 +17,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'PGS Catalog Calculator'
-copyright = '2022, Benjamin Wingfield'
-author = 'Benjamin Wingfield'
+project = 'Polygenic Score (PGS) Catalog Calculator'
+copyright = '2022, PGS Catalog team'
+author = 'Polygenic Score (PGS) Catalog team'
 
 
 # -- General configuration ---------------------------------------------------

docs/index.rst

@@ -3,15 +3,24 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to PGS Catalog Calculator's documentation!
+Welcome to ``pgsc_calc``'s documentation!
 ==================================================
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
 
+   input
+   api
 
 
+``pgsc_calc`` is a bioinformatics best-practice analysis pipeline for applying
+scoring files from the `Polygenic Score (PGS)
+Catalog <https://www.pgscatalog.org/>`_ to target genotyped samples.
+
+.. note::
+
+   This project is under active development and may break at any time.
+
 Indices and tables
 ==================
 

docs/input.rst

@@ -0,0 +1,9 @@
+Input
+======
+
+You need some stuff
+
+JSON
+----
+
+