From 6979eda7260b804099a39b27e417d942feb722b9 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 20 Dec 2021 09:35:58 +1100
Subject: 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).
---
 test-tnpair.nix       | 2 +-
 tools/facets-call.nix | 4 ++--
 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;
-- 
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