diff options
| -rw-r--r-- | tools/gridss.nix | 11 |
1 files changed, 9 insertions, 2 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index 009752e..5bb9484 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -17,6 +17,13 @@ rec { assemble = callBionixE ./gridss-assemble.nix; identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify); annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate); - preprocessBam = input: with samtools; sort {} (gridss.softClipsToSplitReads {} (gridss.computeSamTags {} (sort {nameSort = true;} (gridss.extractSVReads {} (markdup {} (sort {} (fixmate {mateScore = true;} (sort {nameSort = true;} input)))))))); - call = inputs: bionix.gridss.annotateVariants {} (map gridss.preprocessBam inputs); + preprocessBam = with samtools; + pipe [ + (gridss.extractSVReads {}) + (sort {nameSort = true;}) + (gridss.computeSamTags {}) + (gridss.softClipsToSplitReads {}) + (sort {}) + ]; + call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs); } |