diff options
| author | Justin Bedo <cu@cua0.org> | 2021-12-20 09:35:58 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2021-12-20 09:35:58 +1100 |
| commit | 6979eda7260b804099a39b27e417d942feb722b9 (patch) | |
| tree | 212b9b63f7c482abe6f41726186745a5d02ed317 /test-tnpair.nix | |
| parent | cef60e7a0dca226c045641c7a8cc53359c043168 (diff) | |
facets.callCNV: refactor interface
The VCF really is part of config as it's not variants
called on the sample but population variants (like dbsnp).
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 978370c..a08f05d 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -73,7 +73,7 @@ let testNaming = linkOutputs { crai = samtools.index { } (samtools.view { outfmt = types.toCram; } tnpairResult.alignments.tumour); kallisto = kallisto.quant { inherit ref; } (attrValues tnpair.tumour.files); - facets = facets.callCNV { } { vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ]; }; + facets = facets.callCNV { vcf = tnpairResult.platypusVars; } (with tnpairResult.alignments; [ normal tumour ]); cnvkit = cnvkitResults.cnvs; "cnvkit.pdf" = cnvkitResults.plot; "octopus.vcf" = tnpairResult.octopusVars; |