diff options
| author | Justin Bedo <cu@cua0.org> | 2018-11-22 10:43:54 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-11-22 10:43:54 +1100 |
| commit | 24ee2349c16f159f2627665938fd76d599055a9a (patch) | |
| tree | 54a5bce88dc1403f67f58457c2b27882bc32d193 /tools/gridss-softClipsToSplitReads.nix | |
| parent | 90dd48b019ff7bf9e74d202c1deace6a0896cde5 (diff) | |
gridss: fix configure file optional string error
Diffstat (limited to 'tools/gridss-softClipsToSplitReads.nix')
| -rw-r--r-- | tools/gridss-softClipsToSplitReads.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix index 5fce894..1f9c8b4 100644 --- a/tools/gridss-softClipsToSplitReads.nix +++ b/tools/gridss-softClipsToSplitReads.nix @@ -34,8 +34,8 @@ stdenv.mkDerivation rec { I=${input} \ O=$out \ ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \ - ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \ + ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \ WORKER_THREADS=$NIX_BUILD_CORES ''; - passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; } + passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;}; } |