diff options
Diffstat (limited to 'tools/strelka-call.nix')
| -rw-r--r-- | tools/strelka-call.nix | 15 |
1 files changed, 11 insertions, 4 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index ecdea84..bcbb6d1 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -1,6 +1,5 @@ { bionix , nixpkgs -, ref , indexAttrs ? {} , bamIndexAttrs ? {} , flags ? null @@ -10,17 +9,25 @@ with nixpkgs; with lib; +with bionix.types; let filename = path: last (splitString "/" path); + getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f; inputs = [ normal tumour ]; + refs = map getref inputs; + ref = head refs; -in stdenv.mkDerivation { +in + +assert (length (unique refs) == 1); + +stdenv.mkDerivation { name = "strelka"; buildInputs = [ strelka ]; buildCommand = '' - ln -s ${ref.seq} ref.fa - ln -s ${bionix.samtools.faidx indexAttrs ref.seq} ref.fa.fai + ln -s ${ref} ref.fa + ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs} ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} |