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-rw-r--r-- | README.md | 20 | ||||
-rw-r--r-- | example/call.nix | 19 | ||||
-rw-r--r-- | example/default.nix | 42 |
3 files changed, 80 insertions, 1 deletions
@@ -1,2 +1,20 @@ # bionix -Nix functions for use in bioinformatics, and a sample DE analysis + +Bionix is a set of [Nix](http://nixos.org/nix) expressions for specifying and +executing bioinformatics pipelines. It is currently a work in progress, so +documentation is sparse. + +## Getting started + +Install [Nix](http://nixos.org/nix) and then try `nix-build` in the examples +directory. + +## Example pipeline + +The examples directory shows a simple pipeline in the call.nix and default.nix +files. You can build it with `nix-build` in the examples directory. The result +will be linked to ./result, which in this example case is an empty VCF file. + +## Contact + +Please come chat with us at [#bionix:cua0.org](http://matrix.to/#/#bionix:cua0.org). diff --git a/example/call.nix b/example/call.nix new file mode 100644 index 0000000..c9be673 --- /dev/null +++ b/example/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/example/default.nix b/example/default.nix new file mode 100644 index 0000000..bceaa96 --- /dev/null +++ b/example/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;} |