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PGScatalog · May 26, 2022 · 1460389 · 1460389
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diff --git a/.markdownlint.yml b/.markdownlint.yml
diff --git a/conf/base.config b/conf/base.config
@@ -1,41 +1,26 @@
-/*
-========================================================================================
-    nf-core/pgscalc Nextflow base config file
-========================================================================================
-    A 'blank slate' config file, appropriate for general use on most high performance
-    compute environments. Assumes that all software is installed and available on
-    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
-----------------------------------------------------------------------------------------
-*/
-
 process {
-
-    // TODO nf-core: Check the defaults for all processes
+    // defaults for unlabelled processes
+    // however all processes are labelled
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
-    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    memory = { check_max( 2.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
 
     errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
     maxRetries    = 1
     maxErrors     = '-1'
 
-    // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    // reasonable resource limits for medium sized datasets
     withLabel:process_low {
-        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 2.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 1.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
-        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
-        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        cpus   = { check_max( 4     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 8.GB * task.attempt, 'memory'   ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
+    // these lavels are never used except error_retry
     withLabel:process_high {
         cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
         memory = { check_max( 72.GB * task.attempt, 'memory'  ) }

diff --git a/docs/_templates/globaltoc.html b/docs/_templates/globaltoc.html
@@ -0,0 +1,28 @@
+<h3>Contents</h3>
+
+<ul>
+  <li><a href="{{ pathto('index') }}">Home</a></li>
+  <li><a href="{{ pathto('getting-started') }}">Get started</a></li>
+  <li><a href="{{ pathto('how-to/index') }}">How-to guides</a></li>
+  <li><a href="{{ pathto('reference/index') }}">Reference guide</a></li>
+  <li><a href="{{ pathto('explanation/index') }}">Explanation</a></li>
+  <li><a href="{{ pathto('glossary') }}">Glossary</a></li>
+</ul>
+
+<h3>About the project</h3>
+
+<ul>
+  <li><a href="{{ pathto('changelog') }}">Changelog</a></li>
+  <li><a href="{{ pathto('license') }}">License</a></li>
+</ul>
+
+<h3>Useful links</h3>
+
+<ul>
+  <li><a href="https://github.com/pgscatalog/pgsc_calc">Github repository</a></li>
+  <li><a href="https://github.com/pgscatalog/pgsc_calc/issues">Issue tracker</a></li>
+</ul>
+
+<hr>
+<a href="{{ pathto('genindex') }}">Index</a>
+<hr>
diff --git a/docs/api.rst b/docs/api.rst
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -0,0 +1,37 @@
+:orphan:
+
+Changelog
+---------
+
+Versions follow `semantic versioning`_ (``major.minor.patch``). Breaking changes
+will only occur in major versions with changes noted in this changelog.
+
+.. _`semantic versioning`: https://semver.org/
+
+pgsc_calc v0.1.3dev (2022-02-04)
+--------------------------------
+
+Features
+~~~~~~~~
+
+- Simplified JSON input processes
+- Add first draft of documentation
+- Add JSON schemas for validating input data (mostly for web platform)
+
+pgsc_calc v0.1.2dev (2022-01-17)
+--------------------------------
+
+Features
+~~~~~~~~
+
+- Add JSON input support for web platform functionality
+- Set up simple CI tests with Github actions
+
+pgsc_calc v0.1.1dev (2021-12-16)
+--------------------------------
+
+Features
+~~~~~~~~
+
+- First public release
+- Support applying a single scoring file to target genomic data in GrCh37 build
diff --git a/docs/conf.py b/docs/conf.py
@@ -35,7 +35,7 @@
     'sphinxemoji.sphinxemoji'
 ]
 
-sphinxemoji_style = 'twemoji'
+nitpicky = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -56,4 +56,18 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
+
+html_sidebars = {
+    "**": [
+        "search-field.html",
+        "globaltoc.html",
+        "sbt-sidebar-footer.html" ]
+}
+
+html_theme_options = {
+    "repository_url": "https://github.com/pgscatalog/pgsc_calc",
+    "use_repository_button": False,
+    "use_issues_button": False,
+    "extra_navbar": ""
+}
diff --git a/docs/explanation/calculating.rst b/docs/explanation/calculating.rst
@@ -0,0 +1,2 @@
+Calculating polygenic scores
+============================
diff --git a/docs/explanation/goodpractices.rst b/docs/explanation/goodpractices.rst
@@ -0,0 +1,2 @@
+Good practices for polygenic score analysis
+===========================================
diff --git a/docs/explanation/index.rst b/docs/explanation/index.rst
@@ -0,0 +1,15 @@
+:orphan:
+
+Explanation
+===========
+
+.. toctree::
+   :maxdepth: 1
+
+   calculating
+   packaging
+   testing
+   platform   
+   goodpractices
+   troubleshooting
+
diff --git a/docs/explanation/packaging.rst b/docs/explanation/packaging.rst
@@ -0,0 +1,2 @@
+Packaging bioinformatics software with containers
+=================================================
diff --git a/docs/explanation/platform.rst b/docs/explanation/platform.rst
@@ -0,0 +1,2 @@
+Building a web platform for polygenic risk score calculation
+============================================================
diff --git a/docs/troubleshooting.rst → docs/explanation/troubleshooting.rst b/docs/troubleshooting.rst → docs/explanation/troubleshooting.rst
@@ -1,3 +1,5 @@
+.. _troubleshoot:
+
 Troubleshooting
 ===============