update tnpair example to run on colo828

1 files changed, 39 insertions, 17 deletions

diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix
index 51cd703..70f5514 100644
--- a/examples/ex-tnpair/tnpair.nix
+++ b/examples/ex-tnpair/tnpair.nix
@@ -1,26 +1,48 @@
-# This is an example tumour-normal calling pipeline using strelka
-{ bionix ? import ./../.. {}
-, normal
-, tumour
-, ref
-}:
+{bionix ? import <bionix> {}, pair, fetch}:
 
 with bionix;
 with lib;
+with types;
+
+with minimap2;
+with samtools;
+with snpeff;
 
 let
-  input = mapAttrs (_: fetchFastQGZ);
-
-  preprocess = flip pipe [
-    input
-    (bwa.align { ref = fetchFastA ref; })
-    (samtools.fixmate {})
-    (samtools.sort {})
-    (samtools.markdup {})
+  preprocess = s: pipe s [
+    fetch
+    (align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; })
+    (fixmate {})
+    (sort { })
+    (markdup { })
   ];
 
+  dropErrors = input: stage {
+    name = "drop-errors";
+    buildCommand = ''
+      grep -v "ERROR_" ${input} > $out
+    '';
+    passthru.filetype = input.filetype;
+  };
+
+  bams = mapAttrs (_: preprocess) pair;
+
+  variants = let
+    somatic = strelka.callSomatic { } bams; in mapAttrs (_: flip pipe [
+      (compression.uncompress { })
+      (snpeff.annotate { db = ref.grch38.snpeff.db; })
+      dropErrors
+      (snpeff.dbnsfp { dbnsfp = ref.grch38.snpeff.dbnsfp; })
+    ]) {
+      "snvs.vcf" = somatic.snvs;
+      "indels.vcf" = somatic.snvs;
+      "germline.vcf" = strelka.call { } [bams.normal];
+    };
+
+  cnvs = cnvkit.callCNV { } { normals = [ bams.normal ]; tumours = [ bams.tumour ]; };
+
 in linkOutputs {
-  strelka = strelka.callSomatic {} {normal = preprocess normal; tumour = preprocess tumour;};
-  "normal.bam" = preprocess normal;
-  "tumour.bam" = preprocess tumour;
+  inherit variants;
+  alignments = linkOutputs (mapAttrs' (n: nameValuePair (n + ".bam")) bams);
+  cnvkit = cnvs;
 }