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authorJustin Bedo <cu@cua0.org>2021-12-20 09:35:58 +1100
committerJustin Bedo <cu@cua0.org>2021-12-20 09:35:58 +1100
commit6979eda7260b804099a39b27e417d942feb722b9 (patch)
tree212b9b63f7c482abe6f41726186745a5d02ed317
parentcef60e7a0dca226c045641c7a8cc53359c043168 (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).
-rw-r--r--test-tnpair.nix2
-rw-r--r--tools/facets-call.nix4
2 files changed, 3 insertions, 3 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;
diff --git a/tools/facets-call.nix b/tools/facets-call.nix
index 43c4c7f..e1a23c6 100644
--- a/tools/facets-call.nix
+++ b/tools/facets-call.nix
@@ -1,6 +1,6 @@
-{ bionix }:
+{ bionix, vcf }:
-{ vcf, bams }:
+bams:
with bionix;
with types;