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| author | Justin Bedo <cu@cua0.org> | 2019-05-09 14:23:53 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-05-09 14:23:53 +1000 |
| commit | 6137d292d8d721490bf6ded2695cdc71755aff59 (patch) | |
| tree | 7e26b12750b73120509bb886a82bea319ae688ac /test-tnpair.nix | |
| parent | 795c1ce6b03bfa1cefb628026e08371f39b86296 (diff) | |
strelka: rewrite to use multiple outputs
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 6 |
1 files changed, 3 insertions, 3 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 2ea93ae..4d6a794 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -51,9 +51,9 @@ let (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln tnpairResult.variants "strelka") (ln tnpairResult.glvariants "strelka-gl") - (ln (strelka.indels tnpairResult.variants) "strelka.indels.vcf") - (ln (strelka.snvs tnpairResult.variants) "strelka.snvs.vcf") - (ln (strelka.variants tnpairResult.glvariants) "strelka.gl.vcf") + (ln tnpairResult.variants.indels "strelka.indels.vcf") + (ln tnpairResult.variants.snvs "strelka.snvs.vcf") + (ln tnpairResult.glvariants.variants "strelka.gl.vcf") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam") (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam") |