strelka: add germline calling

4 files changed, 52 insertions, 6 deletions

diff --git a/test-tnpair.nix b/test-tnpair.nix
index c531a83..8b268ec 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -15,7 +15,7 @@ let
   sort = samtools.sort {};
   flagstat = samtools.flagstat {};
   check = fastqc.check {};
-  callVariants = strelka.call {};
+  callVariants = strelka.callSomatic {};
   markdup = samtools.markdup {};
   fixmate = samtools.fixmate {};
 
@@ -35,6 +35,7 @@ let
   processPair = { tumour, normal }: rec {
     alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; };
     variants = callVariants alignments;
+    glvariants = strelka.call {} (builtins.attrValues alignments);
     platypusVars = platypus.call {} (builtins.attrValues alignments);
   };
 
@@ -43,6 +44,7 @@ let
   testNaming = linkDrv [
     (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets")
     (ln tnpairResult.variants "strelka")
+    (ln tnpairResult.glvariants "strelka-gl")
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
     (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 8505302..cbdcfb4 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -4,7 +4,7 @@
 , flags ? null
 }:
 
-{normal, tumour}:
+inputs:
 
 with bionix;
 with lib;
@@ -13,7 +13,6 @@ with types;
 let
   filename = path: last (splitString "/" path);
   getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
-  inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
 
@@ -30,9 +29,8 @@ stage {
     ${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
     ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
 
-    configureStrelkaSomaticWorkflow.py \
-      --normalBam ${filename normal}.bam \
-      --tumourBam ${filename tumour}.bam \
+    configureStrelkaGermlineWorkflow.py \
+      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
       --ref ref.fa \
       --runDir $TMPDIR
 
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
new file mode 100644
index 0000000..8505302
--- /dev/null
+++ b/tools/strelka-callSomatic.nix
@@ -0,0 +1,45 @@
+{ bionix
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
+, flags ? null
+}:
+
+{normal, tumour}:
+
+with bionix;
+with lib;
+with types;
+
+let
+  filename = path: last (splitString "/" path);
+  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
+  inputs = [ normal tumour ];
+  refs = map getref inputs;
+  ref = head refs;
+
+in
+
+assert (length (unique refs) == 1);
+
+stage {
+  name = "strelka";
+  buildInputs = with pkgs; [ strelka ];
+  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}
+
+    configureStrelkaSomaticWorkflow.py \
+      --normalBam ${filename normal}.bam \
+      --tumourBam ${filename tumour}.bam \
+      --ref ref.fa \
+      --runDir $TMPDIR
+
+    ./runWorkflow.py \
+      -m local \
+      -j $NIX_BUILD_CORES
+
+    cp -r results $out
+   '';
+}
diff --git a/tools/strelka.nix b/tools/strelka.nix
index 47d5832..04facb9 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -3,5 +3,6 @@
 with bionix;
 
 {
+  callSomatic = callBionixE ./strelka-callSomatic.nix;
   call = callBionixE ./strelka-call.nix;
 }