diff options
| author | Justin Bedo <cu@cua0.org> | 2022-01-17 15:13:28 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2022-01-17 15:13:28 +1100 |
| commit | 8378b7d51381ae3328e0de48c4680c04201e1c84 (patch) | |
| tree | f839f57df9b0a4d4763d1ac265fbe37ee89654d1 | |
| parent | a17cebee7bd7b88427cfde8dc7c15e913b71e936 (diff) | |
snpeff.dbnsfp: paramterise fields
| -rw-r--r-- | tools/snpeff-dbnsfp.nix | 4 |
1 files changed, 3 insertions, 1 deletions
diff --git a/tools/snpeff-dbnsfp.nix b/tools/snpeff-dbnsfp.nix index 003f7f8..ec09f14 100644 --- a/tools/snpeff-dbnsfp.nix +++ b/tools/snpeff-dbnsfp.nix @@ -1,12 +1,14 @@ { bionix , dbnsfp , heapSize ? "31g" +, fields ? [ ] , flags ? "" }: input: with bionix; +with lib; with types; assert (matchFiletype "snpeff-dbnsfp" { vcf = _: true; } input); @@ -17,7 +19,7 @@ stage { buildCommand = '' ln -s ${dbnsfp.db} dbNSFP.txt.gz ln -s ${dbnsfp.index} dbNSFP.txt.gz.tbi - snpsift dbnsfp -db dbNSFP.txt.gz ${input} > $out + snpsift dbnsfp -db dbNSFP.txt.gz ${optionalString (length fields > 0) "-f ${concatStringsSep "," fields}"} ${flags} ${input} > $out ''; buildInputs = with pkgs; [ snpeff ]; passthru.filetype = input.filetype; |