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-rw-r--r--doc/tools-doc.nix1
-rw-r--r--doc/tools.xml1
-rw-r--r--tools/ascat.nix8
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;
}