From 8378b7d51381ae3328e0de48c4680c04201e1c84 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 17 Jan 2022 15:13:28 +1100
Subject: snpeff.dbnsfp: paramterise fields

---
 tools/snpeff-dbnsfp.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

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;
-- 
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