diff options
Diffstat (limited to 'tools/octopus-call.nix')
| -rw-r--r-- | tools/octopus-call.nix | 3 |
1 files changed, 3 insertions, 0 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix index 1688d88..f33d87c 100644 --- a/tools/octopus-call.nix +++ b/tools/octopus-call.nix @@ -28,6 +28,7 @@ assert (length (unique refs) == 1); stage { name = "octopus-call"; buildInputs = with pkgs; [ octopus-caller ]; + outputs = [ "out" "evidence" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${samtools.faidx faidxAttrs ref} ref.fai @@ -35,7 +36,9 @@ stage { ln -s ${i} $(basename ${i}).bam ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai '') inputs} + ${optionalString (length inputs > 1) "mkdir $evidence"} octopus -R ref.fa -I *.bam -o $out \ + --bamout $evidence \ --threads=$NIX_BUILD_CORES \ ${optionalString fast "--fast"} \ ${optionalString very-fast "--very-fast"} \ |