diff options
Diffstat (limited to 'tools/strelka-callSomatic.nix')
| -rw-r--r-- | tools/strelka-callSomatic.nix | 11 |
1 files changed, 4 insertions, 7 deletions
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix index cce6243..ec57b8c 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 = [ "out" "indels" "snvs" ]; + outputs = [ "indels" "snvs" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai @@ -54,13 +54,10 @@ out = stage { sed -i '/^##startTime/d' $g done mv somatic.indels.vcf $indels - ln -s $indels somatic.indels.vcf mv somatic.snvs.vcf $snvs - ln -s $snvs somatic.snvs.vcf - mkdir $out - cp -r * $out ''; passthru.multicore = true; + passthru.filetype = types.filetype.vcf {ref = ref;}; }; -ft = {filetype = types.filetype.vcf {ref = ref;};}; -in out // { indels = out.indels // ft; snvs = out.snvs // ft;} + +in out |