add docs to render on GitHub Pages

.gitignore

@@ -2,3 +2,6 @@
 !.git*
 _*
 *.out
+
+docs/*
+!docs/*.html

README.md

@@ -11,6 +11,7 @@
 This is a modular analysis pipeline for analyzing high-throughput sequencing-based neutralization assays of the type developed in the [Bloom lab](https://research.fredhutch.org/bloom/en.html).
 See **[add link to Loes et al when available]** for a description of these assays.
 That paper is also the scientific citation for this analysis pipeline.
+See [here](https://github.com/jbloomlab/seqneut-pipeline/graphs/contributors) for a list of the contributors to this pipeline.
 
 Essentially, this pipeline goes from the FASTQ files that represent the counts of each barcoded viral variant to the computed neutralization titers for each sera.
 The titers are computed by fitting Hill-curve style neutralization curves using the [neutcurve](https://jbloomlab.github.io/neutcurve/) package; see the documentation for the details of these curves.
@@ -94,6 +95,26 @@ This will almost always be a subdirectory of the same name, so this key will be
 
         seqneut-pipeline: seqneut-pipeline
 
+### docs
+Location where we create the `./docs/` subdirectory with HTMLs for rendering on GitHub pages.
+This will almost always be `docs`, so this key will be as shown below unless you have a good reason to do otherwise:
+
+        docs: docs
+
+### description
+Description of pipeline, used in the HTML docs rendering.
+Should include title (with markdown `#` heading, authors and/or citation, and link to GitHub repo.
+For instance:
+```
+description: |
+  # <title>
+  <short description>
+
+  <authors and/or link to citation>
+
+  See <GitHub repo link> for code and numerical data.
+```
+
 ### viral_libraries
 A dictionary (mapping) of viral library names to CSV files holding these libraries.
 So in general this key will look like:
@@ -432,6 +453,10 @@ You will need to address these QC failures by adjusting `serum_titers_qc_exclusi
 It is expected that you may have to perform several iterations of running and fixing QC failures.
 The pipeline will only run to completion when all all QC filters are passed.
 
+## Rendering HTML plots and notebooks in docs
+If the pipeline runs to completion, it will create HTML documentation with plots of the overall titers, per-serum titer analyses, and per-plate analyses in a docs subdirectory, which will typically named be `./docs/` (if you use suggested key in configuration YAML).
+This HTML documentation can be rendered via [GitHub Pages](https://docs.github.com/en/pages/getting-started-with-github-pages/configuring-a-publishing-source-for-your-github-pages-site) from the `./docs/` directory.
+
 ## Test example and testing via GitHub Actions
 The [./test_example](test_example) subdirectory contains a small test example that illustrates use of the pipeline.
 

docs/index.html

@@ -0,0 +1,26 @@
+<h1 id="test-example-for-seqneut-pipeline">Test example for <a href="https://github.com/jbloomlab/seqneut-pipeline">seqneut-pipeline</a></h1>
+<p>This is a small toy-example created by subsetting a real experiment dataset.</p>
+<p>See <a href="https://github.com/jbloomlab/seqneut-pipeline">https://github.com/jbloomlab/seqneut-pipeline</a>
+for the computer code and underlying numerical data.</p>
+<p>See <a href="https://github.com/jbloomlab/seqneut-pipeline/graphs/contributors">here</a> for a
+list of all contributors to the pipeline.</p>
+<div class="toc"><span class="toctitle">Contents</span><ul>
+<li><a href="#plot-of-titers-for-all-sera">Plot of titers for all sera</a></li>
+<li><a href="#analyses-of-per-serum-neutralization-titers">Analyses of per-serum neutralization titers</a></li>
+<li><a href="#analyses-of-per-plate-counts-and-curve-fits">Analyses of per-plate counts and curve fits</a></li>
+</ul>
+</div>
+<h2 id="plot-of-titers-for-all-sera">Plot of titers for all sera</h2>
+<p><a href="../docs/titers.html">Interactive chart of titers</a></p>
+<h2 id="analyses-of-per-serum-neutralization-titers">Analyses of per-serum neutralization titers</h2>
+<ul>
+<li><a href="../docs/serum_titers_M099d0.html">M099d0</a></li>
+<li><a href="../docs/serum_titers_M099d30.html">M099d30</a></li>
+<li><a href="../docs/serum_titers_Y044d30.html">Y044d30</a></li>
+<li><a href="../docs/serum_titers_Y154d182.html">Y154d182</a></li>
+</ul>
+<h2 id="analyses-of-per-plate-counts-and-curve-fits">Analyses of per-plate counts and curve fits</h2>
+<ul>
+<li><a href="../docs/process_counts_plate2.html">plate2</a></li>
+<li><a href="../docs/process_counts_plate11.html">plate11</a></li>
+</ul>