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| author | Justin Bedo <cu@cua0.org> | 2019-03-22 10:15:10 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-22 10:15:10 +1100 |
| commit | 9ad5160a25975c7457c002a0207820451302fc2d (patch) | |
| tree | 2ff86470a15e6b0f425852133c4981344d712d78 /tools | |
| parent | 72e2b9e39cfb6a78b6b94864d6acfebf7b371376 (diff) | |
cnvkit: add scatter plots
Diffstat (limited to 'tools')
| -rw-r--r-- | tools/cnvkit-scatter.nix | 17 | ||||
| -rw-r--r-- | tools/cnvkit.nix | 5 |
2 files changed, 22 insertions, 0 deletions
diff --git a/tools/cnvkit-scatter.nix b/tools/cnvkit-scatter.nix new file mode 100644 index 0000000..f9dc7f6 --- /dev/null +++ b/tools/cnvkit-scatter.nix @@ -0,0 +1,17 @@ +{bionix +,flags ? null}: + +input: + +with bionix; +with lib; +with types; + +stage { + name = "cnvkit-scatter"; + buildInputs = [ cnvkit.app ]; + buildCommand = '' + cnvkit.py scatter -s ${input}/*.cn{s,r} -o plot.pdf + cp plot.pdf $out + ''; +} diff --git a/tools/cnvkit.nix b/tools/cnvkit.nix index 2259bec..73f4329 100644 --- a/tools/cnvkit.nix +++ b/tools/cnvkit.nix @@ -9,4 +9,9 @@ with bionix; Type: callCNV :: {targets :: target file, annotations :: annotation file, ...} -> {normals :: [bam], tumours :: [bam]} -> CNVs */ callCNV = callBionixE ./cnvkit-batch.nix; + + /* Scatter plot from CNV calls + Type: scatterPlot :: {} -> CNVs -> PDF + */ + scatterPlot = callBionixE ./cnvkit-scatter.nix; } |