From fce03fcbdbea445bc058348db30ccb99274d3f96 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 27 Nov 2018 12:50:46 +1100
Subject: Expand README and add simple example pipeline

---
 example/default.nix | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 example/default.nix

(limited to 'example/default.nix')

diff --git a/example/default.nix b/example/default.nix
new file mode 100644
index 0000000..bceaa96
--- /dev/null
+++ b/example/default.nix
@@ -0,0 +1,42 @@
+# This example uses the pipelines specified in the call.nix file on the
+# synthetic data in this directory.
+with import <bionix> {};
+
+let
+
+  # List of input samples
+  inputs = [
+    # Sample 1
+    {
+      input1 = fetchFastQ {
+        url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample1-1.fq";
+        sha256 = "1m3vc248mbr4v56459q4xsklznssgqb35lwhwk1i9qvxqm7c72nq";
+      };
+
+      input2 =  fetchFastQ {
+      url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample1-2.fq";
+        sha256 = "13fqvdb5r2sidi2i0s3ifg8gyxp8kibpxc3cbiw07d5zcn3g479x";
+      };
+    }
+
+    # Sample 2
+    {
+      input1 = fetchFastQ {
+        url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample2-1.fq";
+        sha256 = "0c6ik4smsw2kb8xbbci80d00c24klk6mqd2a71y4v9hmpnc42fmr";
+      };
+
+      input2 =  fetchFastQ {
+        url = "https://github.com/PapenfussLab/bionix/raw/master/example/sample2-2.fq";
+        sha256 = "0zvrkm2m69lwfi89hzxsbnkp4i6cszh7c624l1qwmd4s6gh7vfcx";
+      };
+    }
+  ];
+
+  # The reference for the synthetic data
+  ref = fetchFastA {
+    url = "https://github.com/PapenfussLab/bionix/raw/master/example/ref.fa";
+    sha256 = "06gphhh40h3mvwvs2m51qc3rpih8mcs8frhd48l94d5bzwfhb2hc";
+  };
+
+in import ./call.nix {inherit inputs ref;}
-- 
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