diff options
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 2 | ||||
| -rw-r--r-- | tools/gridss.nix | 4 |
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); } |