diff options
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 /tools/strelka-call.nix | |
parent | 795c1ce6b03bfa1cefb628026e08371f39b86296 (diff) |
strelka: rewrite to use multiple outputs
Diffstat (limited to 'tools/strelka-call.nix')
-rw-r--r-- | tools/strelka-call.nix | 10 |
1 files changed, 8 insertions, 2 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index bc1e202..dc07291 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -20,9 +20,11 @@ in assert (length (unique refs) == 1); -stage { +let +out = stage { name = "strelka-call"; buildInputs = with pkgs; [ strelka ]; + outputs = [ "out" "variants" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai @@ -48,8 +50,12 @@ stage { sed -i '/^##fileDate/d' $g sed -i '/^##startTime/d' $g done + mv variants.vcf $variants + ln -s $variants variants.vcf mkdir $out cp -r * $out ''; passthru.multicore = true; -} +}; +ft = {filetype = types.filetype.vcf {ref = ref;};}; +in out // { variants = out.variants // ft; } |