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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)
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