deprecate platypusHEADmaster

2 files changed, 0 insertions, 56 deletions

diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
deleted file mode 100644
index 3119006..0000000
--- a/tools/platypus-callVariants.nix
+++ /dev/null
@@ -1,46 +0,0 @@
-{ bionix
-, indexAttrs ? { }
-, bamIndexAttrs ? { }
-, flags ? null
-}:
-
-inputs:
-
-with bionix;
-with lib;
-with types;
-
-
-let
-  filename = path: last (splitString "/" path);
-  getref = matchFiletype "platypus-callVariants" { bam = { ref, ... }: ref; };
-  refs = map getref inputs;
-  ref = head refs;
-in
-
-assert (length (unique refs) == 1);
-
-stage {
-  name = "platypus";
-  buildInputs = with pkgs; [ platypus ];
-  buildCommand = ''
-    ln -s ${ref} ref.fa
-    ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
-    ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
-    ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
-    platypus callVariants \
-      --nCPU=$NIX_BUILD_CORES \
-      --refFile=ref.fa \
-      ${optionalString (flags != null) flags} \
-      -o $out \
-      --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
-
-    # Remove timestamps from output
-    sed -i '/^##fileDate/d' $out
-
-    # Remove platypusOptions from output
-    sed -i '/^##platypusOptions/d' $out
-  '';
-  passthru.filetype = filetype.vcf { inherit ref; };
-  passthru.multicore = true;
-}
diff --git a/tools/platypus.nix b/tools/platypus.nix
deleted file mode 100644
index 29e7e08..0000000
--- a/tools/platypus.nix
+++ /dev/null
@@ -1,10 +0,0 @@
-{ bionix }:
-
-with bionix;
-
-{
-  /* Call variants 
-    Type: { ... } -> [bam] -> vcf
-  */
-  call = callBionixE ./platypus-callVariants.nix;
-}