From dda29ca7685d360d5428dd827d11a9e4139a0872 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 6 Oct 2022 10:21:34 +1100
Subject: init

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+# Day 1 - BioNix Workshop
+
+Let's start by defining *computational reproducibility* as always
+obtaining the same output from a computation given the same inputs. In
+other words, computational reproducibility is about making computations
+*deterministic*.  In the research context, this is important as
+reproducibility allows others (and ourselves) to verify and build upon
+what we have done in future.
+
+# A functional view of things and why Nix is needed
+
+What makes reproducibility difficult is the management of *state*, or
+the context within with a computation takes place. State manipulation is
+widespread:  how many apps updates or system updates do you recall
+automatically being installed over the past year?  Do you think your
+analysis today will be the same in one years time if your software stack
+has changed?
+
+One way to deal with this problem is to make computations *pure* by forbidding
+the use of anything that is not explicitly stated as an input. This is
+the same idea of pure functional programming, only at the higher level of
+executing software.
+
+Nix effectively enforces purity for software execution by ensuring the software
+cannot access anything outside of the specified inputs. By this way, it can
+guarantee a very high degree of reproducibility. Nix is a general build engine
+most commonly used for building software today, but as we will see a bit later
+it can also execute computational biology workflows in a pure manner with a small
+library called BioNix.
+
+# Pipelines in BioNix
+
+```
+# This is an example pipeline specification to do multi-sample variant calling
+# with the Platypus variant caller. Each input is preprocessed by aligning
+# against a reference genome (defaults to GRCH38), fixing mate information, and
+# marking duplicates. Finally platypus is called over all samples.
+{ bionix ? import <bionix> { }
+, inputs
+, ref ? bionix.ref.grch38.seq
+}:
+
+with bionix;
+with lib;
+
+let
+  preprocess = flip pipe [
+    (bwa.align { inherit ref; })
+    (samtools.sort { nameSort = true; })
+    (samtools.fixmate { })
+    (samtools.sort { })
+    (samtools.markdup { })
+  ];
+
+in
+platypus.call { } (map preprocess inputs)
+```
+
+# Nix the language
+
+We will start with learning Nix the langauge, which is used for
+specifying workflows. If you are familar with JSON, it is very similar
+in terms of availble data types but has one very important addition:
+functions. Let's cover the basic data types and their syntax:
+
+- Booleans: `true` and `false`
+- Strings: `"this is a string"`
+- Numbers: `0`, `1.234`
+- Lists: `[ 0 1.234 "string" ]`
+- Attribute sets: `{ a = 5; b = "something else"; }`
+- Comments: `# this is a comment`
+- Functions: `x: x + 1`
+- Variable binding: `let x = 5; in x #=> 5`
+- Function application: `let f = x: x + 1; in f 5 #=> 6`
+- File paths: `/path/to/file`
+
+Some common operators:
+- Boolean conjunctions and disjunctions: `true || false #=> true` `true && false #=> false`
+- Ordering: `3 < 3 #=> false`, `3 <= 3 #=> true`
+- Conditionals: `if 3 < 4 then "a" else "b" #=> a`
+- Addition and subtraction: `3 + 4 #=> 7`, `3 - 4 #=> -1`
+- Multiplication and division: `3 * 4 #=> 12`, `3.0 / 4 #=> 0.75`
+- String concatenation: `"hello " + "world" #=> "hello world"`
+- String interpolation: `"hello ${"world"}" #=> "hello world"`, `"1 + 2 = ${toString (1 + 2)}" #=> "1 + 2 = 3"`
+- Attribute set unions: `{ a = 5; } // { b = 6; } #=> { a = 5; b = 6; }`
+
+# About this interface
+
+This workshop uses [A tour of
+nix](https://github.com/nixcloud/tour_of_nix) with some altered content
+for the purposes of learning enough of Nix the language to write
+workflows in BioNix during the second part. Click next to continue to
+the exercises.
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