snver: require labelled samples

SNVer does not extract sample names from the BAM files and labels the
columns with the input file paths rather than sample names. We rename
the paths to names.

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