13 files changed, 41 insertions, 37 deletions
diff --git a/default.nix b/default.nix
index d607aa2..6e07a74 100644
--- a/default.nix
+++ b/default.nix
@@ -1,13 +1,15 @@
 {nixpkgs ? import <nixpkgs> {}}:
 
 let
-  inherit (nixpkgs) fetchurl;
+  inherit (nixpkgs) fetchurl callPackage;
 
   bionix = nixpkgs.lib.makeExtensible (self:
   let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // attrs);
   in with self; {
     callBionix = callBionix;
     id = x: x;
+    exec = f: x: y: f x y;
+    callBionixE = p: exec (callBionix p);
 
     types = callBionix ./lib/types.nix {};
 
@@ -25,12 +27,14 @@ let
     samtools = callBionix ./tools/samtools.nix {};
     strelka = callBionix ./tools/strelka.nix {};
 
-    qsub = nixpkgs.callPackage ./lib/qsub.nix {};
-    qsubAttr = qsubAttrs: f: attrs: i: qsub qsubAttrs (f attrs i);
-    qsubAttrs = attrs: nixpkgs.lib.mapAttrs (_: x: qsubAttr attrs x);
     ref = callBionix ./lib/references.nix {};
+
+    qsub = attrs: bionix.extend (self: super: with self; rec {
+      qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; } // attrs;
+      qsub = attrs: (callPackage ./lib/qsub.nix {}) (qsubDefs // attrs);
+      exec = f: x: y: qsub (builtins.intersectAttrs qsubDefs x) (f (builtins.removeAttrs x (builtins.attrNames qsubDefs)) y);
+    });
     def = f: defs: attrs: f (defs // attrs);
-    defQsub = qsubAttrs: f: defs: qsubAttr qsubAttrs (def f defs);
 
     # Fetching files of specific type
     fetchFastQ = attrs: with types; tagFiletype (filetype.fq {}) (fetchurl attrs);
diff --git a/lib/qsub.nix b/lib/qsub.nix
index f7b3c3e..77e773f 100644
--- a/lib/qsub.nix
+++ b/lib/qsub.nix
@@ -1,6 +1,6 @@
 {stdenv, lib, writeScript}:
 
-{ ppn ? 1, mem ? 1, walltime ? "24:00:00", tmpDir ? "/tmp" , sleepTime ? 60}: drv: lib.overrideDerivation drv ({ args, builder, name, ... }: {
+{ ppn, mem, walltime, tmpDir, sleepTime}: drv: lib.overrideDerivation drv ({ args, builder, name, ... }: {
   builder = "/bin/bash";
   args = let
     script = writeScript "qsub-script" ''
diff --git a/tools/bowtie.nix b/tools/bowtie.nix
index a9fa2e8..df8f955 100644
--- a/tools/bowtie.nix
+++ b/tools/bowtie.nix
@@ -3,6 +3,6 @@
 with bionix;
 
 {
-  align = callBionix ./bowtie-align.nix;
-  index = callBionix ./bowtie-index.nix;
+  align = callBionixE ./bowtie-align.nix;
+  index = callBionixE ./bowtie-index.nix;
 }
diff --git a/tools/bwa.nix b/tools/bwa.nix
index 1d5215f..ea0e6a0 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -3,6 +3,6 @@
 with bionix;
 
 {
-  align = callBionix ./bwa-mem.nix;
-  index = callBionix ./bwa-index.nix;
+  align = callBionixE ./bwa-mem.nix;
+  index = callBionixE ./bwa-index.nix;
 }
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 1661e95..6e603b2 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -5,5 +5,5 @@ with bionix;
 
 {
   fastqc = callPackage ./fastqc-app.nix {};
-  check = callBionix ./fastqc-check.nix;
+  check = callBionixE ./fastqc-check.nix;
 }
diff --git a/tools/gridss.nix b/tools/gridss.nix
index d47a669..009752e 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -8,15 +8,15 @@ rec {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
-  gridssConfig = callBionix ./gridss-configFile.nix {};
-  callVariants = callBionix ./gridss-callVariants.nix;
-  computeSamTags = callBionix ./gridss-computeSamTags.nix;
-  softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix;
-  collectMetrics = callBionix ./gridss-collectMetrics.nix;
-  extractSVReads = callBionix ./gridss-extractSVReads.nix;
-  assemble = callBionix ./gridss-assemble.nix;
-  identifyVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify;
-  annotateVariants = attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate;
+  gridssConfig = callBionixE ./gridss-configFile.nix {};
+  callVariants = callBionixE ./gridss-callVariants.nix;
+  computeSamTags = callBionixE ./gridss-computeSamTags.nix;
+  softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
+  collectMetrics = callBionixE ./gridss-collectMetrics.nix;
+  extractSVReads = callBionixE ./gridss-extractSVReads.nix;
+  assemble = callBionixE ./gridss-assemble.nix;
+  identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
+  annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
   preprocessBam = input: with samtools; sort {} (gridss.softClipsToSplitReads {} (gridss.computeSamTags {} (sort {nameSort = true;} (gridss.extractSVReads {} (markdup {} (sort {} (fixmate {mateScore = true;} (sort {nameSort = true;} input))))))));
   call = inputs: bionix.gridss.annotateVariants {} (map gridss.preprocessBam inputs);
 }
diff --git a/tools/infercnv.nix b/tools/infercnv.nix
index 518ca76..03e073b 100644
--- a/tools/infercnv.nix
+++ b/tools/infercnv.nix
@@ -5,5 +5,5 @@ with bionix;
 
 {
   app = callPackage ./infercnv-app.nix {};
-  infercnv = callBionix ./infercnv-infer.nix {};
+  infercnv = callBionixE ./infercnv-infer.nix {};
 }
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
index f13f493..8a5d038 100644
--- a/tools/kallisto.nix
+++ b/tools/kallisto.nix
@@ -3,6 +3,6 @@
 with bionix;
 
 {
-  index = callBionix ./kallisto-index.nix;
-  quant = callBionix ./kallisto-quant.nix;
+  index = callBionixE ./kallisto-index.nix;
+  quant = callBionixE ./kallisto-quant.nix;
 }
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index ff940a5..fa1101a 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -3,6 +3,6 @@
 with bionix;
 
 {
-  depth = callBionix ./mosdepth-depth.nix;
-  plot = callBionix ./mosdepth-plot.nix;
+  depth = callBionixE ./mosdepth-depth.nix;
+  plot = callBionixE ./mosdepth-plot.nix;
 }
diff --git a/tools/mutect.nix b/tools/mutect.nix
index 9a8ce41..627b77e 100644
--- a/tools/mutect.nix
+++ b/tools/mutect.nix
@@ -5,5 +5,5 @@ with bionix;
 
 {
   app = callPackage ./mutect-app.nix {inherit (nixpkgs) stdenv fetchurl makeWrapper unzip fetchFromGitHub;};
-  call = callBionix ./mutect-call.nix;
+  call = callBionixE ./mutect-call.nix;
 }
diff --git a/tools/platypus.nix b/tools/platypus.nix
index 0dfe397..1b214dc 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -3,5 +3,5 @@
 with bionix;
 
 {
-  call = callBionix ./platypus-callVariants.nix;
+  call = callBionixE ./platypus-callVariants.nix;
 }
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 62414df..c29db40 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -3,13 +3,13 @@
 with bionix;
 
 {
-  view = callBionix ./samtools-view.nix;
-  faidx = callBionix ./samtools-faidx.nix;
-  flagstat = callBionix ./samtools-flagstat.nix;
-  index = callBionix ./samtools-index.nix;
-  dict = callBionix ./samtools-dict.nix;
-  sort = callBionix ./samtools-sort.nix;
-  merge = callBionix ./samtools-merge.nix;
-  markdup = callBionix ./samtools-markdup.nix;
-  fixmate = callBionix ./samtools-fixmate.nix;
+  view = callBionixE ./samtools-view.nix;
+  faidx = callBionixE ./samtools-faidx.nix;
+  flagstat = callBionixE ./samtools-flagstat.nix;
+  index = callBionixE ./samtools-index.nix;
+  dict = callBionixE ./samtools-dict.nix;
+  sort = callBionixE ./samtools-sort.nix;
+  merge = callBionixE ./samtools-merge.nix;
+  markdup = callBionixE ./samtools-markdup.nix;
+  fixmate = callBionixE ./samtools-fixmate.nix;
 }
diff --git a/tools/strelka.nix b/tools/strelka.nix
index 767c270..d9d97b1 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -3,5 +3,5 @@
 with bionix;
 
 {
-  call = callBionix ./strelka-call.nix;
+  call = callBionixE ./strelka-call.nix;
 }