diff options
Diffstat (limited to 'tools/strelka-call.nix')
-rw-r--r-- | tools/strelka-call.nix | 13 |
1 files changed, 2 insertions, 11 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index e90bdfd..1162558 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -16,14 +16,12 @@ let refs = map getref inputs; ref = head refs; - drv = bionix.strelka.call {inherit indexAttrs bamIndexAttrs flags;} inputs; - in assert (length (unique refs) == 1); stage { - name = "strelka-call"; + name = "strelka"; buildInputs = with pkgs; [ strelka ]; buildCommand = '' ln -s ${ref} ref.fa @@ -32,7 +30,7 @@ stage { ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} configureStrelkaGermlineWorkflow.py \ - ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \ + ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \ --ref ref.fa \ --runDir $TMPDIR @@ -42,11 +40,4 @@ stage { cp -r results $out ''; - passthru.variants = stage { - name = "strelka-call-variants"; - buildCommand = '' - ln -s ${drv}/variants/variants.vcf.gz $out - ''; - passthru.filetype = filetype.gz (filetype.vcf {ref=ref;}); - }; } |