diff options
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | 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; |