7 files changed, 71 insertions, 5 deletions
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
new file mode 100644
index 0000000..456747a
--- /dev/null
+++ b/tools/bowtie-align.nix
@@ -0,0 +1,36 @@
+{ bionix
+, nixpkgs
+, ref
+, bamOutput ? true
+, flags ? null
+, indexAttrs ? {}
+}:
+
+{ input1
+, input2 ? null
+}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+with bionix.compression;
+
+let
+  fa = f: matchFiletype "bowtie2-ref" { fa = _: f; } f;
+  fq = f: matchFiletype "bowtie2-input" { fq = _: f; gz = matchFiletype' "bowtie2-input" { fq = _: f; }; } f;
+
+in stdenv.mkDerivation {
+  name = "bowtie2-align";
+  buildInputs = [ bowtie2 bc ] ++ optional bamOutput samtools;
+  buildCommand = ''
+    cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
+    if [[ $cores -lt 1 ]] ; then
+      cores=1
+    fi
+    bowtie2 -x ${bionix.bowtie.index indexAttrs ref}/ref ${optionalString (flags != null) flags} --threads $cores \
+      ${if input2 != null then "-1 " + fq input1 + " -2 " + fq input2 else "-U " + fq input1} \
+      ${optionalString bamOutput "| samtools view -b"} \
+      > $out
+  '';
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+}
diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
new file mode 100644
index 0000000..98e529f
--- /dev/null
+++ b/tools/bowtie-index.nix
@@ -0,0 +1,22 @@
+{ bionix
+, nixpkgs
+, flags ? null
+, seed ? 42
+}:
+
+ref:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (matchFiletype "bowtie-index" { fa = _: true; } ref);
+
+stdenv.mkDerivation {
+  name = "bowtie-index";
+  buildInputs = [ bowtie2 ];
+  buildCommand = ''
+    mkdir $out
+    bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
+  '';
+}
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
new file mode 100644
index 0000000..a9fa2e8
--- /dev/null
+++ b/tools/bowtie.nix
@@ -0,0 +1,8 @@
+{ bionix, nixpkgs }:
+
+with bionix;
+
+{
+  align = callBionix ./bowtie-align.nix;
+  index = callBionix ./bowtie-index.nix;
+}
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index d5390b9..e0a6f0f 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -5,7 +5,7 @@
 , indexAttrs ? {}
 , assemblyAttrs ? {}
 , collectMetricsAttrs ? {}
-, softClipsToSplitReadsAttrs ? {}
+, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
 , identifyVariantsAttrs ? {}
 , flags ? null
 , config ? null
@@ -47,7 +47,7 @@ let
     ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
   '';
 
-  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs)));
+  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs));
 in
 
 assert (all sorted inputs);
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 00408d6..f57bc12 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -57,5 +57,5 @@ stdenv.mkDerivation rec {
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/
   '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = sort.coord {}; };
+  passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
 }
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 68ea0a5..c5d8062 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -37,5 +37,5 @@ stdenv.mkDerivation rec {
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;};
+  passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
 }
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index e77f3db..37df5c8 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -25,7 +25,7 @@ in stdenv.mkDerivation {
   buildInputs = [ samtools ];
   buildCommand =
     if alreadySorted then
-      "ln -s $out ${input}"
+      "ln -s ${input} $out"
     else
       ''
         samtools sort -@ $NIX_BUILD_CORES \