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| author | Justin Bedo <cu@cua0.org> | 2018-10-04 12:06:54 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-04 12:06:54 +1000 |
| commit | fe68926931b280aaf29808566b49b2e704e8556a (patch) | |
| tree | dad0e9e11852e161c87ea6b7f4f6100a5180b9f2 /tools/strelka-call.nix | |
| parent | 51f3817ecd2ad099b951d11e55eb3e2c516174d3 (diff) | |
Refactor to use bionix tree directly
Diffstat (limited to 'tools/strelka-call.nix')
| -rw-r--r-- | tools/strelka-call.nix | 15 |
1 files changed, 7 insertions, 8 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix index ec7a764..e7fbb58 100644 --- a/tools/strelka-call.nix +++ b/tools/strelka-call.nix @@ -1,15 +1,14 @@ -{ stdenv -, callPackage -, lib -, strelka +{ bionix +, nixpkgs , ref -, index ? callPackage ./samtools-faidx.nix {} -, bamIndex ? callPackage ./samtools-index.nix {} +, indexAttrs ? {} +, bamIndexAttrs ? {} , flags ? null }: {normal, tumour}: +with nixpkgs; with lib; let @@ -21,9 +20,9 @@ in stdenv.mkDerivation { buildInputs = [ strelka ]; buildCommand = '' ln -s ${ref} ref.fa - ln -s ${index ref} ref.fa.fai + 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 ${bamIndex p} ${filename p}.bai") inputs} + ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs} configureStrelkaSomaticWorkflow.py \ --normalBam ${filename normal}.bam \ |