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| author | Justin Bedo <cu@cua0.org> | 2019-03-06 13:25:52 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-06 13:33:16 +1100 |
| commit | be9238d8266682925ae4ad4d291621c03ac38dfd (patch) | |
| tree | 4c38efd2462dcf3c272a746beb85202aa18925c0 | |
| parent | 455e1666a03d9918fe191d1969756d9755a3ecbb (diff) | |
api docs: init ascatNGS
| -rw-r--r-- | doc/tools-doc.nix | 1 | ||||
| -rw-r--r-- | doc/tools.xml | 1 | ||||
| -rw-r--r-- | tools/ascat.nix | 8 |
3 files changed, 10 insertions, 0 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix index e510209..b79f69c 100644 --- a/doc/tools-doc.nix +++ b/doc/tools-doc.nix @@ -24,6 +24,7 @@ stage { nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml" } + docgen ascat 'ascatNGS CNV caller' docgen bowtie 'Bowtie aligner' docgen bwa 'BWA aligner' docgen strelka 'Strelka2 variant caller' diff --git a/doc/tools.xml b/doc/tools.xml index 6b76bf7..5a18670 100644 --- a/doc/tools.xml +++ b/doc/tools.xml @@ -8,6 +8,7 @@ xmlns:xi="http://www.w3.org/2001/XInclude" xml:id="sec-tools"> <title>Tools</title> + <xi:include href="ascat.xml" /> <xi:include href="bowtie.xml" /> <xi:include href="bwa.xml" /> <xi:include href="strelka.xml" /> diff --git a/tools/ascat.nix b/tools/ascat.nix index 05e2299..9e80e4a 100644 --- a/tools/ascat.nix +++ b/tools/ascat.nix @@ -4,6 +4,14 @@ with bionix; { app = pkgs.callPackage ./ascat-app.nix {}; + + /* Generate GC correction file for ascatNGS. + Type: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC) + */ gccorrect = callBionixE ./ascat-gccorrect.nix; + + /* Call CNVs using ascatNGS. Gender is a string as per ascatNGS docs (e.g., "XX"). + Type: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs + */ callCNV = callBionixE ./ascat-callCNV.nix; } |