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| author | Justin Bedo <cu@cua0.org> | 2019-09-06 16:30:22 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-09-06 16:30:22 +1000 |
| commit | daa0a44e0844bdc957a0db1373e194986545eb23 (patch) | |
| tree | 892e477fc794674f37e36829860f6025bac3a821 | |
| parent | 7c61159d7ed296fce82c7518af4a4936e55990fd (diff) | |
strelka: default callSomatic to snvs
| -rw-r--r-- | test-tnpair.nix | 5 | ||||
| -rw-r--r-- | tools/strelka-callSomatic.nix | 4 |
2 files changed, 5 insertions, 4 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 3601a13..f320f58 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -71,9 +71,8 @@ let "cnvkit.pdf" = cnvkitResults.plot; "octopus.vcf" = tnpairResult.octopusVars; "octopus-somatic.vcf" = tnpairResult.octopusSomatic; - #strelka = tnpairResult.variants; - #strelka-indels = tnpairResult.variants.indels; - #"strelka.snvs.vcf" = tnpairResult.variants.snvs; + strelka-indels = tnpairResult.variants.indels; + "strelka.snvs.vcf" = tnpairResult.variants.snvs; "strelka.gl.vcf" = tnpairResult.glvariants; gridss = gridss.callVariants {} (with tnpairResult.alignments; [normal tumour]); gridss2 = gridss.call (with tnpairResult.alignments; [normal tumour]); diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix index fd58d33..b409344 100644 --- a/tools/strelka-callSomatic.nix +++ b/tools/strelka-callSomatic.nix @@ -26,7 +26,7 @@ let out = stage { name = "strelka-callSomatic"; buildInputs = with pkgs; [ strelka ]; - outputs = [ "indels" "snvs" ]; + outputs = [ "out" "indels" "snvs" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai @@ -56,6 +56,8 @@ out = stage { done mv somatic.indels.vcf $indels mv somatic.snvs.vcf $snvs + + ln -s $snvs $out ''; passthru.multicore = true; passthru.filetype = types.filetype.vcf {ref = ref;}; |