diff options
| author | Justin Bedo <cu@cua0.org> | 2019-08-19 10:42:39 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-08-19 10:44:28 +1000 |
| commit | 53f9549eb4957654a18afdb6f5c1049a1eb7ee53 (patch) | |
| tree | ec3439b26f1ec9a523eff137ff5b8cd9fefb9e3c | |
| parent | e303a98cdc8749db939211ee7f691d07371f661a (diff) | |
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.
| -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 |