diff options
| -rw-r--r-- | doc/tools-doc.nix | 1 | ||||
| -rw-r--r-- | doc/tools.xml | 1 | ||||
| -rw-r--r-- | tools/ascat.nix | 4 | ||||
| -rw-r--r-- | tools/facets.nix | 4 |
4 files changed, 8 insertions, 2 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix index a27cde9..5ee8e22 100644 --- a/doc/tools-doc.nix +++ b/doc/tools-doc.nix @@ -28,6 +28,7 @@ stage { docgen bowtie 'Bowtie aligner' docgen bwa 'BWA aligner' docgen cnvkit 'CNVkit CNV caller' + docgen facets 'Facets CNV caller' docgen strelka 'Strelka2 variant caller' mkdir $out diff --git a/doc/tools.xml b/doc/tools.xml index 8eb69ce..33a053b 100644 --- a/doc/tools.xml +++ b/doc/tools.xml @@ -12,6 +12,7 @@ <xi:include href="bowtie.xml" /> <xi:include href="bwa.xml" /> <xi:include href="cnvkit.xml" /> + <xi:include href="facets.xml" /> <xi:include href="strelka.xml" /> </section> </book> diff --git a/tools/ascat.nix b/tools/ascat.nix index 9e80e4a..700cb4e 100644 --- a/tools/ascat.nix +++ b/tools/ascat.nix @@ -6,12 +6,12 @@ with bionix; app = pkgs.callPackage ./ascat-app.nix {}; /* Generate GC correction file for ascatNGS. - Type: {ref :: fasta, chrPrefix :: string, ...} -> (snps :: VCF) -> (gc :: GC) + Type: gccorrect :: {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 + Type: callCNV :: {ref :: fasta, gc :: GC, ...} -> {tumour :: bam, normal :: bam, gender :: string} -> CNVs */ callCNV = callBionixE ./ascat-callCNV.nix; } diff --git a/tools/facets.nix b/tools/facets.nix index ed10ffa..523c72a 100644 --- a/tools/facets.nix +++ b/tools/facets.nix @@ -4,5 +4,9 @@ with bionix; { app = lib.callPackageWith (pkgs // pkgs.rPackages) ./facets-app.nix {}; + + /* Call CNVs + Type: callCnv :: {...} -> {vcf, bams :: [bams]} -> CNVs + */ callCNV = callBionix ./facets-call.nix; } |