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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-12-11 14:17:22 +1100 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-12-11 14:17:22 +1100 |
| commit | f0357e09b8c473b55d22c4632692fcc79021570d (patch) | |
| tree | 9c92993d1f0c788a162159e6440ea958eae3e35d /tools/gridss-annotateVariants.nix | |
| parent | 6742864b8f92f5d7d56da4901486b7e83a271e23 (diff) | |
| parent | 10bdecf6c1338d7f531ddf7b41da14dfe4a4ac33 (diff) | |
Merge branch 'master' of https://github.com/PapenfussLab/bionix
Diffstat (limited to 'tools/gridss-annotateVariants.nix')
| -rw-r--r-- | tools/gridss-annotateVariants.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix index d5390b9..e0a6f0f 100644 --- a/tools/gridss-annotateVariants.nix +++ b/tools/gridss-annotateVariants.nix @@ -5,7 +5,7 @@ , indexAttrs ? {} , assemblyAttrs ? {} , collectMetricsAttrs ? {} -, softClipsToSplitReadsAttrs ? {} +, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } , identifyVariantsAttrs ? {} , flags ? null , config ? null @@ -47,7 +47,7 @@ let ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai ''; - assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs))); + assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs)); in assert (all sorted inputs); |