9 files changed, 97447 insertions, 0 deletions
diff --git a/examples/call.nix b/examples/call.nix
new file mode 100644
index 0000000..c9be673
--- /dev/null
+++ b/examples/call.nix
@@ -0,0 +1,19 @@
+# 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> {}
+,nixpkgs ? import <nixpkgs> {}
+,inputs
+,ref ? null}:
+
+with bionix;
+
+let
+  preprocess = f:
+    samtools.markdup {}
+      (samtools.sort {}
+        (samtools.fixmate {}
+          (bwa.align {ref = if ref == null then bionix.ref.grch38.seq else ref;} f)));
+
+  in platypus.call {} (map preprocess inputs)
diff --git a/examples/default.nix b/examples/default.nix
new file mode 100644
index 0000000..bceaa96
--- /dev/null
+++ b/examples/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;}
diff --git a/examples/ref.fa b/examples/ref.fa
new file mode 100644
index 0000000..fdc51e6
--- /dev/null
+++ b/examples/ref.fa
@@ -0,0 +1,81302 @@
+>SL1344 genome sequence
+agagattacgtctggttgcaagagatcatgacagggggaattggttgaaaataaatatat
+cgccagcagcacatgaacaagtttcggaatgtgatcaatttaaaaatttattgacttagg
+cgggcagatactttaaccaatataggaatacaagacagacaaataaaaatgacagagtac
+acaacatccatgaaccgcatcagcaccaccaccattaccaccatcaccattaccacaggt
+aacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgaacagtgcgg
+gcttttttttcgaccagagatcacgaggtaacaaccatgcgagtgttgaagttcggcggt
+acatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgcc
+aggcaagggcaggtagcgaccgtactttccgcccccgcgaaaattaccaaccatctggtg
+gcaatgattgaaaaaactatcggcggccaggatgctttgccgaatatcagcgatgcagaa
+cgtattttttctgacctgctcgcaggacttgccagcgcgcagccgggattcccgcttgca
+cggttgaaaatggttgtcgaacaagaattcgctcagatcaaacatgttctgcatggtatc
+agcctgctgggtcagtgcccggatagcatcaacgccgcgctgatttgccgtggcgaaaaa
+atgtcgatcgcgattatggcgggacttctggaggcgcgtgggcatcgcgtcacggtgatc
+gatccggtagaaaaattgctggcggtgggccattaccttgaatctaccgtcgatatcgcg
+gaatcgactcgccgtatcgccgccagccagatcccggccgatcacatgatcctgatggcg
+ggctttaccgccggtaatgaaaagggtgaactggtggtgctgggccgtaatggttccgac
+tattccgccgccgtgctggccgcctgtttacgcgctgactgctgtgaaatctggactgac
+gtcgatggcgtgtatacctgtgacccgcgccaggtgccggacgccaggctgctgaaatcg
+atgtcctaccaggaagcgatggaactctcttacttcggcgccaaagtccttcaccctcgc
+accattacgcccatcgcccagttccagatcccctgtctgattaaaaataccggtaatccg
+caggcgccaggaacgctgatcggcgcgtccagcgacgatgataacctgccggttaaaggg
+atctctaaccttaacaacatggcgatgtttagcgtctccggcccgggaatgaaagggatg
+attgggatggcggcgcgtgttttcgccgccatgtctcgcgccgggatctcggtggtgctc
+attacccagtcctcctctgagtacagcatcagtttctgtgtgccgcagagtgactgcgcg
+cgtgcccgccgtgcgatgcaggatgagttctatctggagctgaaagaggggctgctggag
+ccgctggcggttacggagcggttggcgattatctctgttgtcggcgacggtatgcgcacg
+ctacgcggcatttcagcgaaattcttcgccgcgctggcgcgggctaatatcaatatcgtg
+gcgatcgctcagggatcttctgagcgttctatttctgtggtggtgaataacgacgatgcc
+accaccggcgtgcgggtaacgcaccagatgctgttcaataccgatcaggtgattgaagtg
+tttgtcattggcgtcggcggcgtcggcggcgcgctactggaacagcttaaacgtcagcaa
+acctggctgaagaacaagcacatcgatctacgcgtgtgcggcgtggcgaactcaaaggcg
+ttgctaaccaatgtgcatggcctgaatctggacaactggcaggcggaactggcgcaagcg
+aacgcgccgttcaatctgggacgcttaattcgcctggtgaaagaatatcatctactcaat
+ccggtgattgttgattgtacctccagtcaggcggtggccgaccagtatgccgacttcctg
+cgtgaagggttccatgtggtgacgccaaacaagaaagcgaacacctcgtcaatggactac
+taccatcagctacgtttcgccgccgcgcaatcacggcgcaaattcttgtatgacaccaac
+gtcggcgccggtttgccggtaatcgaaaacctgcaaaacctgctgaatgccggtgatgaa
+ctgcaaaaattttccggcattctttccgggtcgctctcttttattttcggtaaactggaa
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+gatccgcgcgacgatctttccggtatggatgtggcgcgtaaactgttgatcctcgcccgc
+gagacgggccgcgagctggagctttccgatattgtgattgaaccggtgttgccgaacgag
+tttgacgcctccggcgatgtgaccgcctttatggcacatctgccgcagcttgacgacgcg
+tttgccgcccgtgtggcgaaagctcgtgatgaaggtaaggtattgcgctatgtgggcaat
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+ttcaaagtgaaaaacggtgaaaacgcgctggcgttctacagccactattatcagcccttg
+ccgttggtgctgcgcggctacggcgcaggcaatgatgtgacggcggcgggcgtgtttgcc
+gatctgttacggaccctctcatggaagttaggagtttaacatggtgaaagtgtatgcccc
+ggcttccagcgcgaacatgagcgtcggtttcgacgtgttgggcgcagccgtcacacccgt
+tgacggcacgttgctgggcgatgtggtatccgttgaagcagcggaccatttccgtctgca
+taacctggggcgatttgccgataaactgccgccggagccgcgtgaaaatattgtttatca
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+aaaaaatatgccgattggttccgggttagggtccagcgcctgttccgtcgtcgccgcgct
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+acgggccattttgcctgcgcagtatcgccgtcaggattgcattgcgcatggacggcatct
+ggccggttttattcacgcctgttactcgcggcagccgcagcttgccgccgcgctgatgaa
+agatgttattgccgaaccataccgcgcgcgtttactgccgggctttagccaggcgcggca
+ggcggtgtcggagatcggcgcgctggcgagcgggatttccgggtcggggccgacgctgtt
+tgcgctatgcgataaaccggagacggcgcagcgcgtcgcggactggctgagcaaacatta
+tctgcaaaatcaggaaggcttcgttcatatttgccggctggatacggcgggcgcacgagt
+agtgggataatcaatgaaactctataatctgaaagaccataatgagcaggtcagctttgc
+gcaggccgtcacgcaaggactgggcaaacagcagggacttttttttccgcacgatctgcc
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+aaagatcctctcggcatttattggcgatgaaataccgcagcaaattctggaagagcgcgt
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+ggcgcgtaaccaactggtgatctccgtccccagcggcaactttggcgatttgacggcagg
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+ggagacgtttagatgggtaaaattattggtatcgacctgggtactaccaactcttgtgta
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