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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 10:30:27 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-12 10:30:27 +1100 |
| commit | 875d5f28926a2dd3e066a4ce08a2ce18baee4661 (patch) | |
| tree | f76116cd6b1a915ece6b1e2435745a420d9eee5a /tools/gridss.nix | |
| parent | f0357e09b8c473b55d22c4632692fcc79021570d (diff) | |
| parent | 979bf4c65ad668b668750b58eefa9996f51b1242 (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index b85e84e..d47a669 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -15,8 +15,8 @@ rec { 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; + identifyVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify; + annotateVariants = 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); } |