deprecate platypusHEADmaster

6 files changed, 10 insertions, 68 deletions

diff --git a/README.md b/README.md
index 9e9536a..adcc91e 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,7 @@ directory and viewing `result/OEBPS/index.html`.
 Several examples are available in `./examples/`. The main example is
 presented in `./examples/default.nix` and can be built using `nix build`
 in `./examples/`. This sample pipeline performs variant calling using
-[`platypus`](https://github.com/andyrimmer/Platypus), alignment using
+[`octopus`](https://github.com/luntergroup/octopus), alignment using
 [`bwa mem`](https://github.com/lh3/bwa), and preprocessing using
 [`samtools`](http://www.htslib.org/).
 
@@ -37,10 +37,10 @@ this pipeline and the other examples.
 
 - The pipeline itself is specified in `examples/call.nix` and
   `examples/default.nix`.
-- The BioNix wrapper to run `platypus` is in
-  `tools/platypus-callVariants.nix`.
-- The Nix expression for the `platypus` software itself can be found in
-  [nixpkgs](https://github.com/NixOS/nixpkgs/blob/master/pkgs/applications/science/biology/platypus/default.nix).
+- The BioNix wrapper to run `octopus` is in
+  `tools/octopus-call.nix`.
+- The Nix expression for the `octopus` software itself can be found in
+  [nixpkgs](https://github.com/NixOS/nixpkgs/blob/master/pkgs/by-name/oc/octopus-caller/package.nix).
 
 ## Constructing workflows
 
diff --git a/default.nix b/default.nix
index cec2b6b..21403a2 100644
--- a/default.nix
+++ b/default.nix
@@ -31,7 +31,6 @@ let
       mutect = callBionix ./tools/mutect.nix { };
       minimap2 = callBionix ./tools/minimap2.nix { };
       picard = callBionix ./tools/picard.nix { };
-      platypus = callBionix ./tools/platypus.nix { };
       ref = callBionix ./lib/references.nix { };
       samtools = callBionix ./tools/samtools.nix { };
       sambamba = callBionix ./tools/sambamba.nix { };
diff --git a/examples/call.nix b/examples/call.nix
index 81a112e..7525835 100644
--- a/examples/call.nix
+++ b/examples/call.nix
@@ -1,7 +1,7 @@
 # This is an example pipeline specification to do multi-sample variant calling
-# with the Platypus variant caller. Each input is preprocessed by aligning
+# with the Octopus variant caller. Each input is preprocessed by aligning
 # against a reference genome (defaults to GRCH38), fixing mate information, and
-# marking duplicates. Finally platypus is called over all samples.
+# marking duplicates. Finally octopus is called over all samples.
 { bionix ? import <bionix> { }
 , inputs
 , ref ? bionix.ref.grch38.seq
@@ -12,7 +12,7 @@ with lib;
 
 let
   preprocess = flip pipe [
-    (bwa.align { inherit ref; })
+    (bwa.align { inherit ref; RG = {SM = "sample"; ID = "sample";};})
     (samtools.sort { nameSort = true; })
     (samtools.fixmate { })
     (samtools.sort { })
@@ -20,4 +20,4 @@ let
   ];
 
 in
-platypus.call { } (map preprocess inputs)
+octopus.call { } (map preprocess inputs)
diff --git a/test-tnpair.nix b/test-tnpair.nix
index ac8d0bb..86496ac 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -58,7 +58,6 @@ with lib; let
       tumours = [alignments.tumour];
     };
     glvariants = strelka.call {} (builtins.attrValues alignments);
-    platypusVars = platypus.call {} (builtins.attrValues alignments);
     octopusVars = octopus.call {} (builtins.attrValues alignments);
     shards = map (x: nameSort (bwa.align {inherit ref;} x)) (shard.fastQPair 2 normal.files);
   };
@@ -94,7 +93,7 @@ with lib; let
   testNaming = linkOutputs {
     crai = samtools.index {} (samtools.view {outfmt = types.toCram;} tnpairResult.alignments.tumour);
     kallisto = kallisto.quant {inherit ref;} (attrValues tnpair.tumour.files);
-    facets = facets.callCNV {vcf = tnpairResult.platypusVars;} (with tnpairResult.alignments; [normal tumour]);
+    facets = facets.callCNV {vcf = tnpairResult.octopusVars;} (with tnpairResult.alignments; [normal tumour]);
     cnvkit = cnvkitResults.cnvs;
     "cnvkit.pdf" = cnvkitResults.plot;
     "octopus.vcf" = tnpairResult.octopusVars;
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;
-}