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author | Justin Bedo <cu@cua0.org> | 2020-09-02 16:24:37 +1000 |
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committer | Justin Bedo <cu@cua0.org> | 2020-09-02 16:24:37 +1000 |
commit | 9cf1724895f001c625fba37d78f517acb6938e07 (patch) | |
tree | cef3900c0ffd13a3e71763d38bd85d893a3ce3ec /tools/gridss-variants.nix | |
parent | f3dc7987e0e841b97fd43160c68f8d09265083bc (diff) |
gridss: shard assembly into 10 pieces by default
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 |