1 files changed, 41 insertions, 40 deletions
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index b409344..6a8f252 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -1,10 +1,10 @@
 { bionix
-, indexAttrs ? {}
-, bamIndexAttrs ? {}
+, indexAttrs ? { }
+, bamIndexAttrs ? { }
 , flags ? null
 }:
 
-{normal, tumour}:
+{ normal, tumour }:
 
 with bionix;
 with lib;
@@ -12,7 +12,7 @@ with types;
 
 let
   filename = path: last (splitString "/" path);
-  getref = f: matchFiletype "strelka-callSomatic" { bam = x: x.ref; } f;
+  getref = matchFiletype "strelka-callSomatic" { bam = x: x.ref; };
   inputs = [ normal tumour ];
   refs = map getref inputs;
   ref = head refs;
@@ -23,44 +23,45 @@ assert (length (unique refs) == 1);
 
 let
 
-out = stage {
-  name = "strelka-callSomatic";
-  buildInputs = with pkgs; [ strelka ];
-  outputs = [ "out" "indels" "snvs" ];
-  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}
+  out = stage {
+    name = "strelka-callSomatic";
+    buildInputs = with pkgs; [ strelka ];
+    outputs = [ "out" "indels" "snvs" ];
+    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
+      configureStrelkaSomaticWorkflow.py \
+        --normalBam ${filename normal}.bam \
+        --tumourBam ${filename tumour}.bam \
+        --ref ref.fa \
+        --runDir $TMPDIR
 
-    ./runWorkflow.py \
-      -m local \
-      -j $NIX_BUILD_CORES
+      ./runWorkflow.py \
+        -m local \
+        -j $NIX_BUILD_CORES
 
-    # Strelka writes runtime stats and timestamps;
-    # both have to be stripped to provide determinism
-    cd results/variants
-    rm *.tbi
-    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 somatic.indels.vcf $indels
-    mv somatic.snvs.vcf $snvs
+      # Strelka writes runtime stats and timestamps;
+      # both have to be stripped to provide determinism
+      cd results/variants
+      rm *.tbi
+      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 somatic.indels.vcf $indels
+      mv somatic.snvs.vcf $snvs
 
-    ln -s $snvs $out
-  '';
-  passthru.multicore = true;
-  passthru.filetype = types.filetype.vcf {ref = ref;};
-};
+      ln -s $snvs $out
+    '';
+    passthru.multicore = true;
+    passthru.filetype = types.filetype.vcf { inherit ref; };
+  };
 
-in out
+in
+out