diff options
Diffstat (limited to 'test-tnpair.nix')
| -rw-r--r-- | test-tnpair.nix | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 7cc5453..6eb2e23 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -11,7 +11,7 @@ let ref = fetchfa ./examples/ref.fa; - alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";}; + alignWithRG = rg: x: nameSort (bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";} x); sort = samtools.sort {}; nameSort = samtools.sort {nameSort = true;}; flagstat = samtools.flagstat {}; @@ -41,7 +41,7 @@ let glvariants = strelka.call {} (builtins.attrValues alignments); platypusVars = platypus.call {} (builtins.attrValues alignments); octopusVars = octopus.call {} (builtins.attrValues alignments); - shards = map (bwa.align {inherit ref;}) (shard.fastQPair 2 normal.files); + shards = map (x: nameSort (bwa.align {inherit ref;} x)) (shard.fastQPair 2 normal.files); }; tnpairResult = processPair tnpair; |