diff options
Diffstat (limited to 'tools/snver-call.nix')
| -rw-r--r-- | tools/snver-call.nix | 8 |
1 files changed, 6 insertions, 2 deletions
diff --git a/tools/snver-call.nix b/tools/snver-call.nix index 5d80719..72562c7 100644 --- a/tools/snver-call.nix +++ b/tools/snver-call.nix @@ -10,9 +10,9 @@ with lib; with types; let - config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${x}\t${toString ploidy}\t1") inputs); + config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${x}\t${toString ploidy}\t1") (attrValues inputs)); getref = f: matchFiletype "SNVer-call" { bam = {ref, ...}: ref; } f; - refs = map getref inputs; + refs = mapAttrsToList (_: getref) inputs; ref = head refs; in @@ -25,6 +25,10 @@ stage { buildCommand = '' SNVerPool -i / -c ${config} -r ${ref} -o snver + for f in *.vcf ; do + ${concatStringsSep "\n" (mapAttrsToList (x: y: "sed -i 's|//${y}|${x}|' $f") inputs)} + done + mkdir $out cp snver.failed.log $log ln -s $log $out/snver.failed.log |