From 6137d292d8d721490bf6ded2695cdc71755aff59 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 9 May 2019 14:23:53 +1000 Subject: strelka: rewrite to use multiple outputs --- tools/strelka-call.nix | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) (limited to 'tools/strelka-call.nix') 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; } -- cgit v1.2.3