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authorJustin Bedo <cu@cua0.org>2022-10-10 13:22:03 +1100
committerJustin Bedo <cu@cua0.org>2022-10-12 09:09:01 +1100
commitac3a4e0363c1fde0f1dbff75b95aa27d9acd5e5e (patch)
tree117083afffdc77dfa0b768901338b93999550bb8 /day2/ex5-bwa/solution.nix
parent059034ab3d5c40c8ef0350c440d4ae343802ec5c (diff)
insert exercise 4
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diff --git a/day2/ex5-bwa/solution.nix b/day2/ex5-bwa/solution.nix
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+{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)