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| author | Justin Bedo <cu@cua0.org> | 2024-11-12 15:50:42 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2024-11-12 15:50:42 +1100 |
| commit | 58fa67ffd09d3bdfe72bef7c873ef94190dc6708 (patch) | |
| tree | 9e382c5b1da76540d6b1ca2d9a053f52042e3579 /test-tnpair.nix | |
| parent | 00d758934e7d5827e01585887a36913a326535ea (diff) | |
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; |