diff options
Diffstat (limited to 'tools/strelka-callSomatic.nix')
-rw-r--r-- | tools/strelka-callSomatic.nix | 13 |
1 files changed, 11 insertions, 2 deletions
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix index cf4b414..cce6243 100644 --- a/tools/strelka-callSomatic.nix +++ b/tools/strelka-callSomatic.nix @@ -21,9 +21,12 @@ in assert (length (unique refs) == 1); -stage { +let + +out = stage { name = "strelka-callSomatic"; buildInputs = with pkgs; [ strelka ]; + outputs = [ "out" "indels" "snvs" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai @@ -50,8 +53,14 @@ stage { sed -i '/^##fileDate/d' $g 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; -} +}; +ft = {filetype = types.filetype.vcf {ref = ref;};}; +in out // { indels = out.indels // ft; snvs = out.snvs // ft;} |