diff options
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 3 |
1 files changed, 1 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index ac8d0bb..86496ac 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -58,7 +58,6 @@ with lib; let tumours = [alignments.tumour]; }; glvariants = strelka.call {} (builtins.attrValues alignments); - platypusVars = platypus.call {} (builtins.attrValues alignments); octopusVars = octopus.call {} (builtins.attrValues alignments); shards = map (x: nameSort (bwa.align {inherit ref;} x)) (shard.fastQPair 2 normal.files); }; @@ -94,7 +93,7 @@ with lib; 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;} (with tnpairResult.alignments; [normal tumour]); + facets = facets.callCNV {vcf = tnpairResult.octopusVars;} (with tnpairResult.alignments; [normal tumour]); cnvkit = cnvkitResults.cnvs; "cnvkit.pdf" = cnvkitResults.plot; "octopus.vcf" = tnpairResult.octopusVars; |