diff options
Diffstat (limited to 'examples')
| -rw-r--r-- | examples/call.nix | 1 | ||||
| -rw-r--r-- | examples/ex-tnpair/tnpair.nix | 1 |
2 files changed, 2 insertions, 0 deletions
diff --git a/examples/call.nix b/examples/call.nix index 8c4f073..8a38fdb 100644 --- a/examples/call.nix +++ b/examples/call.nix @@ -12,6 +12,7 @@ with lib; let preprocess = flip pipe [ (bwa.align { inherit ref; }) + (samtools.sort { nameSort = true; }) (samtools.fixmate {}) (samtools.sort {}) (samtools.markdup {}) diff --git a/examples/ex-tnpair/tnpair.nix b/examples/ex-tnpair/tnpair.nix index 70f5514..9e6befe 100644 --- a/examples/ex-tnpair/tnpair.nix +++ b/examples/ex-tnpair/tnpair.nix @@ -12,6 +12,7 @@ let preprocess = s: pipe s [ fetch (align { preset = "sr"; ref = ref.grch38.seq; flags = "-R'@RG\\tID:${s.type}\\tSM:${s.type}'"; }) + (sort { nameSort = true; }) (fixmate {}) (sort { }) (markdup { }) |