diff options
Diffstat (limited to 'tools/gridss-variants.nix')
| -rw-r--r-- | tools/gridss-variants.nix | 3 |
1 files changed, 2 insertions, 1 deletions
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix index ad4c66d..c208758 100644 --- a/tools/gridss-variants.nix +++ b/tools/gridss-variants.nix @@ -7,6 +7,7 @@ , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; } , config ? null , heapSize ? "4g" +, shards ? 10 }: with bionix; @@ -43,7 +44,7 @@ let ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai ''; - assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs)); + assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.shardedAssemble shards assemblyAttrs inputs)); mkLinks = '' ln -s ${ref} ref.fa |