diff options
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/snver-call.nix | 8 |
2 files changed, 7 insertions, 3 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 0e082d6..7fe5750 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -85,7 +85,7 @@ let "${tnpair.tumour.name}.cram" = samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour); "${tnpair.tumour.name}.fastqc.1" = check-fastqc tnpair.tumour.files.input1; "${tnpair.tumour.name}.fastp" = check-fastp tnpair.tumour.files; - snver = snver.call { ploidy=1; } (with tnpairResult.alignments; [ normal tumour ]); + snver = snver.call { ploidy=1; } tnpairResult.alignments; mosdepth = mosdepth.plot {} { inputs = mapAttrsToList (_: mosdepth.depth {}) tnpairResult.alignments; names = [ "seq1" "seq2" ]; }; inherit alignments; }; diff --git a/tools/snver-call.nix b/tools/snver-call.nix index 5d80719..72562c7 100644 --- a/tools/snver-call.nix +++ b/tools/snver-call.nix @@ -10,9 +10,9 @@ with lib; with types; let - config = pkgs.writeText "pool.txt" (concatMapStringsSep "\n" (x: "${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 |