diff options
| author | Justin Bedo <cu@cua0.org> | 2019-12-17 12:30:38 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-12-17 12:32:45 +1100 |
| commit | 4a7f5bfd34f53906901059c501aff9b5459eccf8 (patch) | |
| tree | 19a6f0b0596be2971d95ef73de15390e21dcafc0 | |
| parent | c48e7b40c82326006136463282b803eebc648df0 (diff) | |
delly: init
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -rw-r--r-- | tools/delly.nix | 7 |
3 files changed, 9 insertions, 0 deletions
diff --git a/default.nix b/default.nix index 7ad804f..a7b9c52 100644 --- a/default.nix +++ b/default.nix @@ -41,6 +41,7 @@ let hisat2 = callBionix ./tools/hisat2.nix {}; xenomapper = callBionix ./tools/xenomapper.nix {}; manta = callBionix ./tools/manta.nix {}; + delly = callBionix ./tools/delly.nix {}; slurm = attrs: bionix.extend (self: super: with self; rec { slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs; diff --git a/test-tnpair.nix b/test-tnpair.nix index 49c9bb9..8d9dc88 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -74,6 +74,7 @@ let strelka-indels = tnpairResult.variants.indels; "strelka.snvs.vcf" = tnpairResult.variants.snvs; "strelka.gl.vcf" = tnpairResult.glvariants; + delly = delly.call {} (with tnpairResult.alignments; [normal tumour]); manta = manta.call {} (with tnpairResult.alignments; {normals = [normal tumour]; }); mantaTN = manta.call {} (with tnpairResult.alignments; {normals = [normal]; tumour = tumour;}); mantaT = manta.call {} (with tnpairResult.alignments; {tumour = tumour;}); diff --git a/tools/delly.nix b/tools/delly.nix new file mode 100644 index 0000000..9bac4c6 --- /dev/null +++ b/tools/delly.nix @@ -0,0 +1,7 @@ +{ bionix }: + +with bionix; + +{ + call = callBionixE ./delly-call.nix; +} |