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| author | Justin Bedo <cu@cua0.org> | 2019-03-06 13:28:41 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-06 13:33:16 +1100 |
| commit | abb7760edbc301256db6fc50b5fd475175bd7606 (patch) | |
| tree | e370320aa11919ac87a4b276224d6f9ac687148f | |
| parent | be9238d8266682925ae4ad4d291621c03ac38dfd (diff) | |
api docs: init CNVkit
| -rw-r--r-- | doc/tools-doc.nix | 1 | ||||
| -rw-r--r-- | doc/tools.xml | 1 | ||||
| -rw-r--r-- | tools/cnvkit.nix | 6 |
3 files changed, 7 insertions, 1 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix index b79f69c..a27cde9 100644 --- a/doc/tools-doc.nix +++ b/doc/tools-doc.nix @@ -27,6 +27,7 @@ stage { docgen ascat 'ascatNGS CNV caller' docgen bowtie 'Bowtie aligner' docgen bwa 'BWA aligner' + docgen cnvkit 'CNVkit CNV caller' docgen strelka 'Strelka2 variant caller' mkdir $out diff --git a/doc/tools.xml b/doc/tools.xml index 5a18670..8eb69ce 100644 --- a/doc/tools.xml +++ b/doc/tools.xml @@ -11,6 +11,7 @@ <xi:include href="ascat.xml" /> <xi:include href="bowtie.xml" /> <xi:include href="bwa.xml" /> + <xi:include href="cnvkit.xml" /> <xi:include href="strelka.xml" /> </section> </book> diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix index 610b18c..2259bec 100644 --- a/tools/cnvkit.nix +++ b/tools/cnvkit.nix @@ -3,6 +3,10 @@ with bionix; { -app = lib.callPackageWith (pkgs // pkgs.pythonPackages) ./cnvkit-app.nix {}; + app = lib.callPackageWith (pkgs // pkgs.pythonPackages) ./cnvkit-app.nix {}; + + /* Call CNVs + Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs + */ callCNV = callBionixE ./cnvkit-batch.nix; } |