diff options
| author | Justin Bedo <cu@cua0.org> | 2018-12-18 14:05:19 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-12-18 14:11:57 +1100 |
| commit | 0418c23f5d3bff108744d96d1075b0e76b580fdd (patch) | |
| tree | 4a77565abe39bba1dc93139f2d4539496a041198 /tools/gridss.nix | |
| parent | 2ec0e115917d194eeea6ef4c1b4b1f7f6a7f416b (diff) | |
qsub: refactor overriding
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 18 |
1 files changed, 9 insertions, 9 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index d47a669..009752e 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -8,15 +8,15 @@ rec { url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar"; sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; }; - gridssConfig = callBionix ./gridss-configFile.nix {}; - 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 = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify; - annotateVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate; + gridssConfig = callBionixE ./gridss-configFile.nix {}; + callVariants = callBionixE ./gridss-callVariants.nix; + computeSamTags = callBionixE ./gridss-computeSamTags.nix; + softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix; + collectMetrics = callBionixE ./gridss-collectMetrics.nix; + extractSVReads = callBionixE ./gridss-extractSVReads.nix; + 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); } |