diff options
Diffstat (limited to 'tools/octopus-call.nix')
-rw-r--r-- | tools/octopus-call.nix | 37 |
1 files changed, 37 insertions, 0 deletions
diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix new file mode 100644 index 0000000..f88960c --- /dev/null +++ b/tools/octopus-call.nix @@ -0,0 +1,37 @@ +{ bionix +, faidxAttrs ? {} +, indexAttrs ? {} +, flags ? ""}: + +with bionix; +with lib; +with types; + +inputs: + +let + getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f; + refs = map getref inputs; + ref = head refs; + +in + +assert (length (unique refs) == 1); + +stage { + name = "octopus-call"; + buildInputs = with pkgs; [ octopus-caller ]; + buildCommand = '' + ln -s ${ref} ref.fa + ln -s ${samtools.faidx faidxAttrs ref} ref.fai + ${concatMapStringsSep "\n" (i: '' + ln -s ${i} $(basename ${i}).bam + ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai + '') inputs} + octopus -R ref.fa -I *.bam -o $out \ + --threads=$NIX_BUILD_CORES \ + ${flags} + ''; + passthru.filtype = filetype.vcf {ref = ref;}; + passthru.multicore = true; +} |