1 files changed, 39 insertions, 38 deletions
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 74dfd0b..6a84b24 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,6 +1,6 @@
 { bionix
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
@@ -12,7 +12,7 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "strelka-call" { bam = x: x.ref; } f;
+  getref = matchFiletype "strelka-call" { bam = x: x.ref; };
   refs = map getref inputs;
   ref = head refs;
 
@@ -21,38 +21,39 @@ in
 assert (length (unique refs) == 1);
 
 let
-out = stage {
-  name = "strelka-call";
-  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}
-
-    configureStrelkaGermlineWorkflow.py \
-      ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
-      --ref ref.fa \
-      --runDir $TMPDIR
-
-    ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES 2>&1
-
-    # Strelka writes runtime stats and timestamps;
-    # both have to be stripped to provide determinism
-    cd results/variants
-    rm *.tbi genome.vcf.gz
-    for f in *.vcf.gz; do
-      gunzip $f
-      g=$(basename $f .gz)
-      sed -i '/^##fileDate/d' $g
-      sed -i '/^##startTime/d' $g
-      sed -i '/^##cmd/d' $g
-    done
-    mv variants.vcf $out
-  '';
-  passthru.multicore = true;
-  passthru.filetype = types.filetype.vcf {ref = ref;};
-};
-in out
+  out = stage {
+    name = "strelka-call";
+    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}
+
+      configureStrelkaGermlineWorkflow.py \
+        ${concatMapStringsSep " " (i: "--bam ${filename i}.bam") inputs} \
+        --ref ref.fa \
+        --runDir $TMPDIR
+
+      ./runWorkflow.py \
+        -m local \
+        -j $NIX_BUILD_CORES 2>&1
+
+      # Strelka writes runtime stats and timestamps;
+      # both have to be stripped to provide determinism
+      cd results/variants
+      rm *.tbi genome.vcf.gz
+      for f in *.vcf.gz; do
+        gunzip $f
+        g=$(basename $f .gz)
+        sed -i '/^##fileDate/d' $g
+        sed -i '/^##startTime/d' $g
+        sed -i '/^##cmd/d' $g
+      done
+      mv variants.vcf $out
+    '';
+    passthru.multicore = true;
+    passthru.filetype = types.filetype.vcf { inherit ref; };
+  };
+in
+out