insert exercise 4

4 files changed, 0 insertions, 92 deletions

diff --git a/day2/ex4-bwa/default.nix b/day2/ex4-bwa/default.nix
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--- a/day2/ex4-bwa/default.nix
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@@ -1,52 +0,0 @@
-/*
-BioNix is a thin wrapper over Nix: there is not much functionality
-required for pipelining that is not already present in the base build
-engine. As such, the focus is on providing an interface that is
-convenient for specifying common bioinformatics workflows. To this end,
-BioNix provides a library of tools to help simplify the specification of
-common bioinformatics pipelines, with a notable focus on genomics tools.
-You can see the available tools at
-https://github.com/PapenfussLab/bionix/tree/master/tools.
-
-This exercise aims to demonstrate how to both use a tool available in
-BioNix on some input data and how to chain them together. We will do a
-simple alignment with BWA on some simulated reads from a bacterial
-genome. The BWA tool is provided by
-https://github.com/PapenfussLab/bionix/blob/master/tools/bwa.nix and as
-you can see there are alignment functions for alignment with BWA/BWA2,
-as well as corresponding index functions for indexing a reference
-genome.  Don't worry about indexing, this will be handled automatically,
-you only have to declare you want an alignment and what genome and the
-index will be generated if needed.
-
-Exercise:
-
-1. Sample data along with a reference will be fetched from github. As
-before, hashes of the content must be known. Fill in the hashes to fully
-specify the inputs.
-
-2. With the hashes in place, the expression should evaluate and BWA
-should run.  Try swapping BWA out with some of the other available
-aligners in BioNix (e.g., bowtie, hisat2, minimap2, whisper).
-
-3. Aligners produce *unsorted* output, but co-ordinate sorted alignments
-are usually desired as they are indexable by position. Pass the aligned
-output to the samtools sort function to sort the alignments into co-
-ordinate order.
-*/
-{bionix}:
-with bionix; let
-  input = {
-    input1 = fetchFastQ {
-      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/sample1-1.fq";
-    };
-    input2 = fetchFastQ {
-      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/sample1-2.fq";
-    };
-  };
-
-  ref = fetchFastA {
-    url = "https://raw.githubusercontent.com/PapenfussLab/bionix/bac9248a5e08e8afdf5485a6e27cfe72e1ca5090/examples/ref.fa";
-  };
-in
-  bwa.align {} input
diff --git a/day2/ex4-bwa/flake.lock b/day2/ex4-bwa/flake.lock
deleted file mode 120000
index 981422e..0000000
--- a/day2/ex4-bwa/flake.lock
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@@ -1 +0,0 @@
-../../common/flake.lock
\ No newline at end of file
diff --git a/day2/ex4-bwa/flake.nix b/day2/ex4-bwa/flake.nix
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--- a/day2/ex4-bwa/flake.nix
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-{
-  inputs = {
-    nixpkgs.url = "github:nixos/nixpkgs";
-    bionix.url = "github:papenfusslab/bionix";
-    flake-utils.url = "github:numtide/flake-utils";
-  };
-
-  outputs = {
-    self,
-    nixpkgs,
-    bionix,
-    flake-utils,
-  }:
-    flake-utils.lib.eachDefaultSystem (system: let
-      pkgs = import nixpkgs {inherit system;};
-      bionix' = import bionix {nixpkgs = pkgs;};
-    in {
-      defaultPackage = bionix'.callBionix ./. {};
-    });
-}
diff --git a/day2/ex4-bwa/solution.nix b/day2/ex4-bwa/solution.nix
deleted file mode 100644
index 79fc7dc..0000000
--- a/day2/ex4-bwa/solution.nix
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@@ -1,19 +0,0 @@
-{bionix}:
-with bionix; let
-  input = {
-    input1 = fetchFastQ {
-      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/sample1-1.fq";
-      sha256 = "sha256-qE6s8hKowiz3mvCq8/7xAzUz77xG9rAcsI2E50xMAk4=";
-    };
-    input2 = fetchFastQ {
-      url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/sample1-2.fq";
-      sha256 = "sha256-s02R49HX/qeJp4t/eZwsKwV9D07uLGId8CEpU2dB8zM=";
-    };
-  };
-
-  ref = fetchFastA {
-    url = "https://raw.githubusercontent.com/PapenfussLab/bionix/master/examples/ref.fa";
-    sha256 = "sha256-V3zqOJFuGtukDRQttK/pGfKofgOlKrridHaWYhGGyWs=";
-  };
-in
-  samtools.sort {} (bwa.align {inherit ref;} input)