ascat: init

1 files changed, 36 insertions, 0 deletions

diff --git a/tools/ascat-gccorrect.nix b/tools/ascat-gccorrect.nix
new file mode 100644
index 0000000..c1838d9
--- /dev/null
+++ b/tools/ascat-gccorrect.nix
@@ -0,0 +1,36 @@
+{ bionix
+, ref
+, chrPrefix ? ""
+, flags ? null
+}:
+
+snp:
+
+with bionix;
+with lib;
+with types;
+
+stage rec {
+  name = "ascat-gccorrect";
+  buildInputs = with pkgs; [ ascat.app gawk ];
+  script = pkgs.writeText "convert.awk" ''
+    BEGIN{
+      FS = OFS = "\t"
+    }
+    /^#/{next}
+    !loc[$1,$2]{
+      print $3, "${chrPrefix}" $1, $2
+      loc[$1,$2]++
+    }
+  '';
+  buildCommand = ''
+    awk -f ${script} ${snp} > snpPos.tsv
+    mkdir splitPos splitGc splitGcLogs
+    split --number=l/$NIX_BUILD_CORES -d snpPos.tsv splitPos/snpPos.
+    ls -1 splitPos/ | xargs -n1 -P$NIX_BUILD_CORES -I '{}' sh -c 'ascatSnpPanelGcCorrections.pl ${ref} splitPos/{} > splitGc/{}'
+    mv splitGc/snpPos.00 $out
+    for f in splitGc/* ; do
+      sed 1d $f >> $out
+    done
+  '';
+}