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Diffstat (limited to 'tools/octopus-callSomatic.nix')
| -rw-r--r-- | tools/octopus-callSomatic.nix | 3 |
1 files changed, 3 insertions, 0 deletions
diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix index 5c2ca90..d3e7f96 100644 --- a/tools/octopus-callSomatic.nix +++ b/tools/octopus-callSomatic.nix @@ -42,6 +42,7 @@ assert (length (unique refs) == 1); stage { name = "octopus-callSomatic"; buildInputs = with pkgs; [ octopus-caller samtools ]; + outputs = [ "out" "evidence" ]; buildCommand = '' ln -s ${ref} ref.fa ln -s ${samtools.faidx faidxAttrs ref} ref.fai @@ -50,7 +51,9 @@ stage { ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai '') inputs} normal=$(samtools view -H ${normal} | awk -f ${smScript}) + mkdir $evidence octopus -R ref.fa -I *.bam -o $out \ + --bamout $evidence \ --threads=$NIX_BUILD_CORES \ ${optionalString fast "--fast"} \ ${optionalString very-fast "--very-fast"} \ |