From 6666e4a997a6fc468a492fdfe15522fd993c9a6a Mon Sep 17 00:00:00 2001
From: Marina Gourtovaia <mg8@sanger.ac.uk>
Date: Tue, 9 Jan 2024 14:57:38 +0000
Subject: [PATCH] README update

---
 MANIFEST  |  2 ++
 README    | 30 +-----------------------------
 README.md | 45 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 48 insertions(+), 29 deletions(-)
 mode change 100644 => 120000 README
 create mode 100644 README.md

diff --git a/MANIFEST b/MANIFEST
index 6ac8f04bd..af114f860 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -166,6 +166,8 @@ lib/npg_qc/utils/bam_genotype.pm
 lib/npg_qc/utils/genotype_calling.pm
 MANIFEST
 README
+README.md
+README_QC.md
 scripts/npgqc_dbix_schema_loader.pl
 t/00-critic.t
 t/00-distribution.t
diff --git a/README b/README
deleted file mode 100644
index a64bbc01b..000000000
--- a/README
+++ /dev/null
@@ -1,29 +0,0 @@
-QC Checks and Metrics for Illumina Next Generation Sequencing Data
-==================================================================
-
-lib directory:
----------------
- npg_qc::Schema namespace - DBIx db binding
- npg_qc::illumina - db loaders for Illumina QC metrics
- npg_qc::autoqc namespace - WTSI core sequencing pipeline inhouse
-     QC checks and storage of QC results
-
-bin directory:
---------------
- perl scripts
-
-scripts directory:
-------------------
- supplimentary scripts
-
-src directory:
---------------
- Moved to https://github.com/wtsi-npg/npg_qc_utils
-
-t directory:
-------------
- tests
- test data
- supplimentary scripts and modules for testing
-
-
diff --git a/README b/README
new file mode 120000
index 000000000..42061c01a
--- /dev/null
+++ b/README
@@ -0,0 +1 @@
+README.md
\ No newline at end of file
diff --git a/README.md b/README.md
new file mode 100644
index 000000000..012e67aa3
--- /dev/null
+++ b/README.md
@@ -0,0 +1,45 @@
+# QC Checks and Metrics for Illumina Next Generation Sequencing Data
+
+## Listing of Directories
+
+### lib
+
+ - npg_qc::Schema namespace - DBIx ORM
+ - npg_qc::illumina namespace - db loaders for Illumina QC metrics
+ - npg_qc::autoqc namespace - WSI core sequencing pipeline in-house
+     QC checks and storage of QC metrics
+ - npg_qc::mqc - evaluation and reporting of QC metrics
+
+### bin
+
+Perl scripts which are deployed to the production environment
+
+### scripts
+
+Suppliementary scripts, not deployed
+
+### t
+
+Tests, test data, supplementary scripts and modules for testing
+
+### npg_qc_viewer
+
+Source code for the web server that displays the QC metrics
+
+### docs
+
+Documentation, useful code snippets
+
+## NPG QC database
+
+### Legacy Data
+
+QC metrics and evaluation outcomes for all production Illumina sequencing runs
+are stored in a relational database. This database has four legacy tables,
+`recipe_file`, `run_and_pair`, `run_info`, `run_recipe`, for which we do not
+generate ORM classes. No code is using these tables. The data is kept for
+auditing perposes. The size of these tables is small in comparison with the size
+of the rest of the tables. The overhead of moving these old tables to a different
+storage is not justified.
+
+