From 5e508d19fb2927574229df09b64c3fbfc2b752eb Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 19 Dec 2018 16:46:19 +1100
Subject: examples: added example tumour-normal calling pipeline script

---
 examples/call.nix     |    19 +
 examples/default.nix  |    42 +
 examples/ref.fa       | 81302 ++++++++++++++++++++++++++++++++++++++++++++++++
 examples/sample1-1.fq |  4000 +++
 examples/sample1-2.fq |  4000 +++
 examples/sample2-1.fq |  4000 +++
 examples/sample2-2.fq |  4000 +++
 examples/tnpair       |    58 +
 examples/tnpair.nix   |    26 +
 9 files changed, 97447 insertions(+)
 create mode 100644 examples/call.nix
 create mode 100644 examples/default.nix
 create mode 100644 examples/ref.fa
 create mode 100644 examples/sample1-1.fq
 create mode 100644 examples/sample1-2.fq
 create mode 100644 examples/sample2-1.fq
 create mode 100644 examples/sample2-2.fq
 create mode 100755 examples/tnpair
 create mode 100644 examples/tnpair.nix

(limited to 'examples')

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
+gaggggatgagtctctcacaggcgaccgccctggcgcgcgagatgggctataccgaaccc
+gatccgcgcgacgatctttccggtatggatgtggcgcgtaaactgttgatcctcgcccgc
+gagacgggccgcgagctggagctttccgatattgtgattgaaccggtgttgccgaacgag
+tttgacgcctccggcgatgtgaccgcctttatggcacatctgccgcagcttgacgacgcg
+tttgccgcccgtgtggcgaaagctcgtgatgaaggtaaggtattgcgctatgtgggcaat
+atcgaagaggatggcgtgtgccgcgtgaaaattgccgaagttgatggtaacgatccgctc
+ttcaaagtgaaaaacggtgaaaacgcgctggcgttctacagccactattatcagcccttg
+ccgttggtgctgcgcggctacggcgcaggcaatgatgtgacggcggcgggcgtgtttgcc
+gatctgttacggaccctctcatggaagttaggagtttaacatggtgaaagtgtatgcccc
+ggcttccagcgcgaacatgagcgtcggtttcgacgtgttgggcgcagccgtcacacccgt
+tgacggcacgttgctgggcgatgtggtatccgttgaagcagcggaccatttccgtctgca
+taacctggggcgatttgccgataaactgccgccggagccgcgtgaaaatattgtttatca
+gtgctgggaacgtttttgccaggcattggggaaaaccatcccggtggcgatgacgctgga
+aaaaaatatgccgattggttccgggttagggtccagcgcctgttccgtcgtcgccgcgct
+ggtcgcgatgaatgagcactgcggcaaaccgttaaacgacacgcgtctgttggcgctgat
+gggcgagctggaaggccgtatctccggcagcatccattacgataacgtcgcgccgtgctt
+tcttggcggtatgcagttgatgattgaagaaaacggcattattagtcagcaggtgccggg
+ctttgatgagtggctatgggtactggcttatccgggcattaaagtttctaccgcagaagc
+acgggccattttgcctgcgcagtatcgccgtcaggattgcattgcgcatggacggcatct
+ggccggttttattcacgcctgttactcgcggcagccgcagcttgccgccgcgctgatgaa
+agatgttattgccgaaccataccgcgcgcgtttactgccgggctttagccaggcgcggca
+ggcggtgtcggagatcggcgcgctggcgagcgggatttccgggtcggggccgacgctgtt
+tgcgctatgcgataaaccggagacggcgcagcgcgtcgcggactggctgagcaaacatta
+tctgcaaaatcaggaaggcttcgttcatatttgccggctggatacggcgggcgcacgagt
+agtgggataatcaatgaaactctataatctgaaagaccataatgagcaggtcagctttgc
+gcaggccgtcacgcaaggactgggcaaacagcagggacttttttttccgcacgatctgcc
+ggagtttagcctgacggaaattgatgagatgctcaaccaggactttgtcagccgtagcgc
+aaagatcctctcggcatttattggcgatgaaataccgcagcaaattctggaagagcgcgt
+ccgcgcggcgtttgcgttcccggcaccggtagcgcaggtagaaagcgatgtcggctgcct
+ggagctgttccatggtccgacgctggcctttaaagacttcggcgggcgttttatggcgca
+aatgctgacgcatatcagcggcgacaaaccggtgacgattctgactgcaacgtcaggcga
+taccggcgcggcggtggctcacgcgttctatggcctggaaaatgtgcgggtcgtcattct
+ctacccgcgcggtaagatcagtccgttgcaggaaaaactgttctgtacgctgggcggcaa
+cattgaaaccgtggcgatcgacggcgatttcgacgcgtgccaggcgctggtgaaacaggc
+atttgatgacgaagaactgaaaacggcgctggggctgaattcggctaattcgattaatat
+cagccgcctgttggcgcaaatttgctactactttgaagccgtggcgcaactgccgcaggg
+ggcgcgtaaccaactggtgatctccgtccccagcggcaactttggcgatttgacggcagg
+gctgctggcgaagtcgttaggcctaccggtgaaacgttttatcgccgccaccaacgtcaa
+cgacacggtgccgcgttttctgcatgacggaaagtgggcgccgaaagcgacgcaggcgac
+cctgtcgaatgcgatggatgtcagccagccgaataactggccgcgcgtggaggagctatt
+ccgccgtaaaatctggcgcctgactgagctgggctatgcggcggtggatgatactacgac
+acagcagacgatgcgcgagctgaaagcgaaaggttatatctcggaacctcatgcggcggt
+agcgtatcgggcattacgcgaccagttaaaccctggcgagtatggcttgtttctcggaac
+ggcgcatccggcgaagtttaaagagagcgtggagtccattctgggagaaacgctggcctt
+gcctgaagcgctcgccgaacgcgccgacctgccgctgctttcacatcatctgcctgcgga
+ttttgccgccctgcgtaagctgatgatgacccgccaataaccattgcgcccggtggcgct
+gtcgcttaccgggcctatggggtggtgtcgatttgtaggccggataaggcgtaaccgcca
+tccggcgatgccgttactgctcgtagcgtttaaagaccagctcgtcttgtgtggaggttt
+cttcatcaaagaaatacccttcacggtcaaacgcggtaagctgttccggcttcgttaagc
+ggttttcaataataaaacggctcatcagtccgcgcgcttttttggcgtagaagcttacca
+ccttaaacttgccgtttttctcatcaaggaacacgggcttaatcagttcggcattcagtt
+tcttcggcttcaccgatttaaaatattcctcggaggccagattcaccaccacccgatcgc
+cctgcgcctcaagcgcttcgttgagcttatcggtaatgatatcgccccagaattgataaa
+gatctttgccgcgcggattctccaggcgaatccccatctccagacgataaggctgcatta
+aatccagcgggcgcaatacgccatacaagccagagagcatacgcagatgttgttgagcaa
+aatcaaaatccgcgtcgttgaacgtttccgcctgtaggccggtataaacatcgcctttga
+acgccagaatcgcctggcgtgcattatccggcgtaaaatgaggctgccagtcatgaaaac
+gcgtggcgttgagatccgccagtttgtcgctaattcccatcagcctggaaatttgcggcg
+ccgaaagctggcgggcctgttgaataagctgctggctgtgatccaacagctccggctggg
+tatagcgggtcgtggccagcgggctttgataatcaagcgtttttgcaggtgaaatcagaa
+tcagcatattcagtccttgcagggaattttctgcgactttagcaaaaaaacgccgcagag
+ttgaccgatggttgcgattgtcggcttaatcgcgcgatgccgcctcccaggtatctggcg
+ccagttgtggttcgatatccgggaagcgccgcggatcgaactgcggtcttacgcccagtt
+tccgttgtcgcagataatcgctggcgagggtatacaccaccggtgagagcaacaaaatcg
+ccgtcagattggtaatggccatacaggccatgatcatgtcagcgagctgccatatcagcg
+gaaaactgataagcgtaccggcgataaccatgccaagcgtcgcaaggcgtaatagccaga
+tagcctttgcgttatgtaaccgcagaaaaaacagattgttttcggcgtaaatatagttgg
+cgacgatagaactgaacgcgaacagaatgacgataagcgcgacaaaactggcgccccatt
+caccggtcaacgaaaccattgcatgttggagaagctgaatgccttctgttgacgagtggg
+acgcgtgattccccgccagcaggataatcatcgcgctggcggtacagatgataatggtgt
+cgctgaatacgccaatcatttgcacaatcccctgcgcgacagggtgagggggatacgacg
+ttgccgctgcggccgcattaggcgttgaccccattcccgcttcattagagaacatcccac
+gctgaaaaccgctggtaatagcctgggtgagcgtatatccggctgcgcctgccgcggctt
+cctgccagccaaatgcgcttttgactatcgaggcgataacgccaggcatttgctcaatat
+gccagaggcaaatgaatacgctgccggcgacccacaataacgcgatgaggggaatcagcc
+attgcatcagacgggcgacgcctttgatgccgcgaatgataattaacagggcacagaacg
+ccagagcaatgccggagataagcggcggaatgttgaaggcgaaatggagcgcgcgtgaga
+cggcattcgcctgcacgctattaaaaatcaacccgtaggcgacgagcagaaagagggcga
+aaaccacgcccatccagcgcattcccagcccacgcgccatataccacgccgggccgccgc
+ggaactggcctgtcgggtcacgttctttataaagctgggcaagcgaacactcggcgaagg
+aggtcgccatgccaatgatggccgagacccacatccagaataccgcgccgggaccgcctg
+cggcgatagccagcgccacgccggccaggttaccgctgccaatccgcgccgcgaggctgg
+tacacagagcctgaaatgacgtcaggccgcctggctgcgggctaaggctgcctttcagac
+tgcggctaaattggcgaatataacgaaactgaatgaatccggtacgccaggtaaaccaac
+atcctgcgccgagcagcaggtaaatcattaccgagccccagagtatttcgttaataaaac
+tgaaaaactcaggcattaacgtccctcttgttgatgccggcacgctttgataatcctgta
+taagcgtgacccatgatgtagatgaccttgtcagactaatattaacggcagtttaccata
+aatacggtggtatcctttaattgcgcatcaaccgtcggcagatacgcaaacagtgcacaa
+gggcagccaggtgcatgtaggcggttgcgctgtgagtgcgtcgtgttatcatcagggtag
+accggttacatcccctaacaagctgtttaaagagaaactctatcatgacggacaaattga
+cctcccttcgtcagttcaccaccgtagtggctgataccggagatatcgcggcaatgaaac
+tgtatcagccgcaggatgctacaactaacccttctctcattcttaacgcagcgcaaatcc
+cggaatatcgtaagctgattgacgatgctgtcgcctgggcgaaacagcagagcagcgacc
+gcgcgcagcaggttgttgacgcgaccgataagctggcggtgaatattggcctggagatcc
+tgaagctggtgccggggcgtatttctaccgaagttgacgcgcgtctgtcttatgacactg
+aagcgtctatcgccaaagcaaaacgtatcattaaactctacaatgatgcgggtatcagca
+acgatcgtatcctgatcaagctggcgtccacctggcagggcattcgtgcagccgaacagc
+tggaaaaagaaggcatcaactgtaacctgacgctgctgttctccttcgcgcaggcgcgtg
+cgtgcgccgaagcgggcgtctacctgatctcgccgttcgtaggtcgtattcttgactggt
+ataaagccaataccgacaagaaagactatgcgccagctgaagatccgggcgtggtttccg
+taacggaaatctacgagtactacaaacagcatggttacgaaaccgtcgttatgggcgcaa
+gcttccgtaacgtaggcgaaattctggagctggcgggctgcgaccgtctgactatcgcgc
+cggcattgctgaaagaactggcggaaagcgaaggggcgattgagcgtaagctctctttct
+ccggcgaagtcaaagcgcgcccggaacgcattaccgaagccgagttcctgtggcagcatc
+accaggaccccatggcggttgacaaactggcggatggtatccgtaagtttgcggtagacc
+aggaaaaactggaaaaaatgatcggcgatctgctgtaatcattaacgcgtggccctgata
+tgggtcacgctacctcttctgaaacctgtctgtccttcccttcgcagtgtatcattctgt
+ttaacgagactgtttaaacggaataatcatggataccttacgtattggcttagtttctat
+ctccgaccgcgcttcaagcggcgtttaccaggataaaggcattcctgcgcttgaggagtg
+gctcgcttctgcgctgaccacgcctttcgaggtccaacggcgcttaattcctgatgaaca
+ggaaattatcgagcaaacgttgtgtgaactggtcgatgagatgagctgtcatctggtgct
+gaccactggcggtaccggtccggcgcgtcgcgacgtcacgccggacgcgacccttgccat
+cgccgaccgtgaaatgccaggttttggcgagcagatgcgccagatcagcctgcgctttgt
+gccgaccgccattctttcccgccaggtgggcgttatccgtaaacaggcgttaattcttaa
+tctgcctggacagccaaaatcgatcaaagaaacgctggaaggcgtaaaagcggacgatgg
+cagcgttagcgtgccgggcatttttgcgagcgtgccgtattgcatacagctgcttgacgg
+gccgtatgtcgaaaccgcgccggaagtggttgccgctttccgtccaaagagcgccagacg
+tgagaatatgtcggactgaccggaaaatactgatagtagggttattcctcccggtgcggg
+aggaataaaagagatttagtgcgcctcgccgattggcagaatagtgcggccaaattgctc
+gtttagcacttcacccatcgccagataaatagcgctggcgccgcaaaccagaccaaccca
+gcctgcgatatggatagttgcttcgttaccggtgatattgccgaccgccagcagagcgaa
+cagtacggtcaggctcaggaaaacaaattgcagcgcgcgggcggctttcagcgtaccgaa
+gaacataaacagcgtgaacacgccccacagacctaaataagcgccgagtagctgagcgtc
+aggcgcatccgtcagacccattttcggcatcagcaggatagcgaccagcgtcagccagaa
+cgaaccgtaagaggtaaaggccgttaaaccaaaggtattgccttttttgtactccagcag
+accggcaaaaatttgcgcgataccgccgtagaaaatccccatcgccagaataataccgtc
+cagggcgaaaaaaccggcattgtgcaggttaagcagaatggtggtcatgccgaagcccat
+caggcccagcggtgccggattagccaacttagtgttgcccataattcctcaaaatcatca
+taattgaatggtgaaatagtttcccagaataacgagttccgtattcggggcgcggcataa
+taatcagggggaagaggactgtctatgatctaataagggggaaaagaaaatatttccccc
+agtgagggcattcacgcctgaacggctgccatcattcgtcgcaggcaggctatttgcaag
+accgccggaatagtcacgcgatacgcgctgccgctcatcgctttgacgccgtttaacgcc
+gcgccgaccgggccgccaagacctgcgccgcgcagcaatccgtggcccaggatgctcatt
+gcggcatgggtacgcaaaatgcgggtaagctgggtggaaagcaggtgggagacccctttt
+gccagactgcgatctttcatgagcagcggcagcagttcttccagttcagaaactttggcg
+tctacggcttgcagaaattcctgcttatgcgccgcgtccatcttctgccaggtatgacgt
+aaaaaatgctccagcagttgctgttctatttcaaacgtcgacatgcttttatctgctttg
+agttttagccgttttgcgacatccagcagaatcgcgcggtactgttttccgtgtccgcgc
+aatttgttggcgatactgtcgccgccgtaatgctgaaactcgccggcaatgagctgccag
+ttacggcggtgttgctccgggtgaccttccatcgctttgaacagctcgttatggctaaga
+acgctcgacaagcgagctttgcccttttcgttatgcgtcagcaaacgggcgaaatcggcg
+agttgttcttcgctacaatgctgaagaaagtctaaatcctcgtcgtgtaaataggtgacg
+ttcattttcagtctggcttttggaatagaaataacagcgattaatcgtcgccaatgactt
+taagtctcgccatatcggaagaatttaccgtatggcctgagaaggtaatctttgatacgc
+agcgtttgttgtcgttatcgctattaatattgatccagcctgttgtctggccctctttga
+ttgaggaagggacgttcaggctttggctggcgctacgcgcagttttaaaatagacggatg
+cgccgctaagttcgatgtcgccgtgatccgccgtgagttgaatgcgcttcacgatgcggc
+agacgggaattttcagcgtgagatcgttcgtttcatttctgggcatggcaataacaccca
+gtattttatggtcgttcgcgtgcgcgacgctacttaacgccaggccgaaaagcaggccga
+cggaaatcgttaacacagatcgcatggaatttctctttgacgggttcaataagcaatacc
+gtctatcatactctgctcatggcaacgattcagttttgtaatcttttctttttattacaa
+tttttctgtgaatggtattcgttatttaatttatttcatgaatatttatctgtctggttt
+tccatcgtgccctctcgtcactaaaaaattttttcatctcccccttgatgacgtgggtta
+cgaccccatcttgtagtcaaccgcagtggtgagtctgaaaaaaaacgattcagggtagtt
+gaaaccgcacgtttcgcccttattacagattcacaaccacatgatgaccgaatttttagt
+ggagacgtttagatgggtaaaattattggtatcgacctgggtactaccaactcttgtgta
+gcgattatggatggaacgcaggcacgcgtgctggagaacgccgagggcgatcgcactacg
+ccttctatcattgcttatacccaggatggtgaaactctggttggtcagccggctaaacgt
+caggcagtgacaaacccgcaaaacaccctgtttgcgattaaacgcctgattggccgccgc
+ttccaggacgaagaagttcaacgtgacgtttctatcatgccgtacaaaatcatcggcgcc
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