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authorJustin Bedo <cu@cua0.org>2019-03-06 13:35:41 +1100
committerJustin Bedo <cu@cua0.org>2019-03-06 13:35:41 +1100
commitd52ef1a0189015ea463628391e8877bc0c1d11a5 (patch)
treedce6e234f6b31785bd049acadf01473df60f3b3f
parent8fa9b007544a37b2674a2eb87978652e14fbd2b3 (diff)
api doc: init fastqc
-rw-r--r--doc/tools-doc.nix1
-rw-r--r--doc/tools.xml1
-rw-r--r--tools/fastqc.nix4
3 files changed, 6 insertions, 0 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix
index 5ee8e22..f52f6ad 100644
--- a/doc/tools-doc.nix
+++ b/doc/tools-doc.nix
@@ -29,6 +29,7 @@ stage {
docgen bwa 'BWA aligner'
docgen cnvkit 'CNVkit CNV caller'
docgen facets 'Facets CNV caller'
+ docgen fastqc 'FastQC quality control'
docgen strelka 'Strelka2 variant caller'
mkdir $out
diff --git a/doc/tools.xml b/doc/tools.xml
index 33a053b..2592b48 100644
--- a/doc/tools.xml
+++ b/doc/tools.xml
@@ -13,6 +13,7 @@
<xi:include href="bwa.xml" />
<xi:include href="cnvkit.xml" />
<xi:include href="facets.xml" />
+ <xi:include href="fastqc.xml" />
<xi:include href="strelka.xml" />
</section>
</book>
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 5632958..6279682 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -4,5 +4,9 @@ with bionix;
{
fastqc = pkgs.callPackage ./fastqc-app.nix {};
+
+ /* QC check
+ Type: check :: {...} -> input :: fastq -> report
+ */
check = callBionixE ./fastqc-check.nix;
}