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author | Justin Bedo <cu@cua0.org> | 2018-12-19 16:46:19 +1100 |
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committer | Justin Bedo <cu@cua0.org> | 2018-12-19 16:46:19 +1100 |
commit | 5e508d19fb2927574229df09b64c3fbfc2b752eb (patch) | |
tree | 6af14e192521cb3cd127d51dc1f502d3700d241d /examples/default.nix | |
parent | a458b2813b2b0749e801098fe8aa03d8444141a6 (diff) |
examples: added example tumour-normal calling pipeline script
Diffstat (limited to 'examples/default.nix')
-rw-r--r-- | examples/default.nix | 42 |
1 files changed, 42 insertions, 0 deletions
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;} |