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-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
-rw-r--r--tools/gridss.nix4
2 files changed, 3 insertions, 3 deletions
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 35cd7b4..b35d41d 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -21,7 +21,7 @@ assert (matchFileSorting "gridss-softClipsToSplitReads" { name = _: true; } inpu
stdenv.mkDerivation rec {
name = "gridss-softClipsToSplitReads";
- buildInputs = [ jre ];
+ buildInputs = [ jre bwa ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
diff --git a/tools/gridss.nix b/tools/gridss.nix
index bc2f0b8..1e4e2d1 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -17,6 +17,6 @@ rec {
assemble = callBionix ./gridss-assemble.nix;
identifyVariants = callBionix ./gridss-identifyVariants.nix;
annotateVariants = callBionix ./gridss-annotateVariants.nix;
- preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input)))));
- call = inputs: annotateVariants {} (map preprocessBam inputs);
+ preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input)))));
+ call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs);
}