diff options
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 16 |
1 files changed, 15 insertions, 1 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index 7a2f217..d46a8ce 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -1,7 +1,21 @@ {bionix, nixpkgs}: +with nixpkgs; with bionix; -{ +rec { + jar = fetchurl { + url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar"; + sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; + }; callVariants = callBionix ./gridss-callVariants.nix; + computeSamTags = callBionix ./gridss-computeSamTags.nix; + softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix; + collectMetrics = callBionix ./gridss-collectMetrics.nix; + extractSVReads = callBionix ./gridss-extractSVReads.nix; + 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); } |