diff options
Diffstat (limited to 'tools/gridss-softClipsToSplitReads.nix')
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index d480328..93d02df 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -30,12 +30,13 @@ stage rec { java -Xmx${heapSize} -Dsamjdk.create_index=false \ -cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \ VERBOSITY=WARNING \ - REFERENCE_SEQUENCE=ref.fa \ - I=${input} \ - O=$out \ + REFERENCE_SEQUENCE=ref.fa \ + I=${input} \ + O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \ - WORKER_THREADS=$NIX_BUILD_CORES + WORKER_THREADS=$NIX_BUILD_CORES \ + ${optionalString (flags != null) flags} ''; passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; }; passthru.multicore = true; |