aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorJustin Bedo <cu@cua0.org>2019-12-17 12:30:38 +1100
committerJustin Bedo <cu@cua0.org>2019-12-17 12:32:45 +1100
commit4a7f5bfd34f53906901059c501aff9b5459eccf8 (patch)
tree19a6f0b0596be2971d95ef73de15390e21dcafc0
parentc48e7b40c82326006136463282b803eebc648df0 (diff)
delly: init
-rw-r--r--default.nix1
-rw-r--r--test-tnpair.nix1
-rw-r--r--tools/delly.nix7
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;
+}