Add files generated docs

docs/files-generated.rst

@@ -0,0 +1,96 @@
+.. _files_generated:
+
+===============
+Files Generated
+===============
+
+Here, we provide a list of all files generated by MIPTools and a brief
+description of each file. This list aims to assist users in determining the
+most useful output for downstream analysis.
+
+Non-aggregate Tables
+====================
+
+alternate_table
+	insert description
+
+coverage_table
+	insert description
+
+genotypes_table
+	insert description
+
+reference_table
+	insert description
+
+Aggregate Amino Acid Changes
+============================
+
+alternate_AA_table
+	insert description
+
+coverage_AA_table
+	insert description
+
+genotypes_AA_table
+	insert description
+
+reference_AA_table
+	insert description
+
+Aggregate Nucleotide Changes
+============================
+
+alternate_AN_table
+	insert description
+
+coverage_AN_table
+	insert description
+
+genotypes_AN_table
+	insert description
+
+reference_AN_table
+	insert description
+
+Haplotype Files
+===============
+
+aligned_haplotypes
+	insert description
+
+all_haplotypes
+	insert description
+
+haplotype_counts
+	insert description
+
+mapped_haplotypes
+	insert description
+
+offtarget_haplotypes
+	insert description
+
+unique_haplotypes
+	insert description
+
+Barcode Files
+=============
+
+all_barcode_counts
+	insert description
+
+barcode_counts
+	insert description
+
+Sequence Run Files
+==================
+
+repool
+	insert description
+
+run_meta
+	insert description
+
+sample_summary
+	insert description

docs/index.rst

@@ -13,6 +13,12 @@ inversion probe design, data processing, and analysis.
    installation
    quick_start
 
+.. toctree::
+  :caption: Glossary
+  :maxdepth: 1
+
+  files-generated
+
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