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-rw-r--r--default.nix25
-rw-r--r--test-tnpair.nix12
-rw-r--r--tools/bwa-index.nix6
-rw-r--r--tools/bwa-mem.nix15
-rw-r--r--tools/bwa.nix6
-rw-r--r--tools/crumble-toCram.nix12
-rw-r--r--tools/crumble.nix4
-rw-r--r--tools/fastqc-check.nix12
-rw-r--r--tools/fastqc.nix4
-rw-r--r--tools/gridss-callVariants.nix20
-rw-r--r--tools/gridss.nix4
-rw-r--r--tools/mosdepth-depth.nix14
-rw-r--r--tools/mosdepth-plot.nix10
-rw-r--r--tools/mosdepth.nix6
-rw-r--r--tools/platypus-callVariants.nix14
-rw-r--r--tools/samtools-faidx.nix7
-rw-r--r--tools/samtools-flagstat.nix7
-rw-r--r--tools/samtools-index.nix7
-rw-r--r--tools/samtools-sort.nix7
-rw-r--r--tools/samtools.nix10
-rw-r--r--tools/strelka-call.nix15
-rw-r--r--tools/strelka.nix4
22 files changed, 110 insertions, 111 deletions
diff --git a/default.nix b/default.nix
index 10d2249..9f96a9d 100644
--- a/default.nix
+++ b/default.nix
@@ -2,18 +2,21 @@
let
bionix = nixpkgs.lib.makeExtensible (self:
- let callBionix = file: import file { bionix = self; nixpkgs = nixpkgs; };
- in with self; {
- bwa = callBionix ./tools/bwa.nix;
- crumble = callBionix ./tools/crumble.nix;
- fastqc = callBionix ./tools/fastqc.nix;
- gridss = callBionix ./tools/gridss.nix;
- mosdepth = callBionix ./tools/mosdepth.nix;
- platypus = callBionix ./tools/platypus.nix;
- samtools = callBionix ./tools/samtools.nix;
- strelka = callBionix ./tools/strelka.nix;
+ let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // attrs);
+ in with self; {
+ callBionix = callBionix;
+ id = x: x;
+
+ bwa = callBionix ./tools/bwa.nix {};
+ crumble = callBionix ./tools/crumble.nix {};
+ fastqc = callBionix ./tools/fastqc.nix {};
+ gridss = callBionix ./tools/gridss.nix {};
+ mosdepth = callBionix ./tools/mosdepth.nix {};
+ platypus = callBionix ./tools/platypus.nix {};
+ samtools = callBionix ./tools/samtools.nix {};
+ strelka = callBionix ./tools/strelka.nix {};
qsub = nixpkgs.callPackage ./lib/qsub.nix {};
- ref = callBionix ./lib/references.nix;
+ ref = callBionix ./lib/references.nix {};
});
in bionix
diff --git a/test-tnpair.nix b/test-tnpair.nix
index ef2af1b..77b5727 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -1,11 +1,19 @@
with (import <nixpkgs> {});
-with (import <bionix> {});
with lib;
let
+ bionix = (import <bionix> {}).extend (self: super: {
+ bwa = super.bwa // { index = attrs: super.bwa.index ({ flags = "-a is" ; } // attrs); };
+ });
+
+in
+
+with bionix;
+
+let
ref = ./example/ref.fa;
alignWithRG = rg: bwa.align { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
- sort = samtools.sort { };
+ sort = samtools.sort {};
flagstat = samtools.flagstat {};
check = fastqc.check {};
callVariants = strelka.call { inherit ref; };
diff --git a/tools/bwa-index.nix b/tools/bwa-index.nix
index 3329221..3f9d385 100644
--- a/tools/bwa-index.nix
+++ b/tools/bwa-index.nix
@@ -1,11 +1,11 @@
-{ stdenv
-, lib
-, bwa
+{ bionix
+, nixpkgs
, flags ? null
}:
ref:
+with nixpkgs;
with lib;
stdenv.mkDerivation {
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 9af3992..6e83a6d 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -1,21 +1,16 @@
-{ stdenv
-, callPackage
-, lib
-, bc
-, bwa
-, index ? callPackage ./bwa-index.nix { inherit bwa stdenv lib; }
-, samtools ? null
+{ bionix
+, nixpkgs
, ref
, bamOutput ? true
, flags ? null
+, indexAttrs ? {}
}:
{ input1
, input2 ? null
}:
-assert bamOutput -> samtools != null;
-
+with nixpkgs;
with lib;
stdenv.mkDerivation {
@@ -23,7 +18,7 @@ stdenv.mkDerivation {
buildInputs = [ bwa bc ] ++ optional bamOutput samtools;
buildCommand = ''
ln -s ${ref} ref.fa
- for f in ${index ref}/* ; do
+ for f in ${bionix.bwa.index indexAttrs ref}/* ; do
ln -s $f
done
cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc)
diff --git a/tools/bwa.nix b/tools/bwa.nix
index df61cba..1d5215f 100644
--- a/tools/bwa.nix
+++ b/tools/bwa.nix
@@ -1,8 +1,8 @@
{ bionix, nixpkgs }:
-with nixpkgs;
+with bionix;
{
- align = attrs: callPackage ./bwa-mem.nix attrs;
- index = attrs: callPackage ./bwa-index.nix attrs;
+ align = callBionix ./bwa-mem.nix;
+ index = callBionix ./bwa-index.nix;
}
diff --git a/tools/crumble-toCram.nix b/tools/crumble-toCram.nix
index 6b2431f..2544e17 100644
--- a/tools/crumble-toCram.nix
+++ b/tools/crumble-toCram.nix
@@ -1,15 +1,15 @@
-{ stdenv
-, lib
-, callPackage
-, crumble ? callPackage ./crumble-app.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
+with nixpkgs;
with lib;
input:
stdenv.mkDerivation {
name = "crumble";
- buildInputs = [ crumble ];
+ buildInputs = [ bionix.crumble.crumble ];
buildCommand = "crumble ${optionalString (flags != null) flags} ${input} $out";
}
diff --git a/tools/crumble.nix b/tools/crumble.nix
index 4798329..fb48c8f 100644
--- a/tools/crumble.nix
+++ b/tools/crumble.nix
@@ -1,7 +1,9 @@
{ bionix, nixpkgs }:
with nixpkgs;
+with bionix;
{
- toCram = attrs: callPackage ./crumble-toCram.nix attrs;
+ crumble = callPackage ./crumble-app.nix {};
+ toCram = callBionix ./crumble-toCram.nix;
}
diff --git a/tools/fastqc-check.nix b/tools/fastqc-check.nix
index 1d9993a..17d6183 100644
--- a/tools/fastqc-check.nix
+++ b/tools/fastqc-check.nix
@@ -1,16 +1,16 @@
-{ stdenv
-, lib
-, callPackage
-, fastqc ? callPackage ./fastqc-app.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
+with nixpkgs;
with lib;
input:
stdenv.mkDerivation {
name = "fastqc-check";
- buildInputs = [ fastqc ];
+ buildInputs = [ bionix.fastqc.fastqc ];
buildCommand = ''
mkdir $out
fastqc \
diff --git a/tools/fastqc.nix b/tools/fastqc.nix
index 2034c91..1661e95 100644
--- a/tools/fastqc.nix
+++ b/tools/fastqc.nix
@@ -1,7 +1,9 @@
{ bionix, nixpkgs }:
with nixpkgs;
+with bionix;
{
- check = attrs: callPackage ./fastqc-check.nix attrs;
+ fastqc = callPackage ./fastqc-app.nix {};
+ check = callBionix ./fastqc-check.nix;
}
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 9d78896..e431560 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -1,15 +1,11 @@
-{ stdenv
-, lib
-, callPackage
-, fetchurl
-, jre
-, R
-, bwa
+{ bionix
+, nixpkgs
, ref
, blacklist ? null
-, bwaIndex ? callPackage ./bwa-index.nix { inherit stdenv bwa lib; }
-, faidx ? callPackage ./samtools-faidx.nix { inherit stdenv; }
-, flags ? null}:
+, bwaIndexAttrs ? {}
+, faidxAttrs ? {}
+, flags ? null
+}:
with lib;
@@ -24,8 +20,8 @@ stdenv.mkDerivation rec {
};
buildCommand = ''
ln -s ${ref} ref.fa
- ln -s ${faidx ref} ref.fa.fai
- for f in ${bwaIndex ref}/*; do
+ ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
+ for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
ln -s $f
done
mkdir $out
diff --git a/tools/gridss.nix b/tools/gridss.nix
index fa52606..edf9f57 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,7 +1,7 @@
{bionix, nixpkgs}:
-with nixpkgs;
+with bionix;
{
- callVariants = attrs: callPackage ./gridss-callVariants.nix attrs;
+ callVariants = callBiolnix ./gridss-callVariants.nix;
}
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index be28aaf..7043c43 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -1,10 +1,10 @@
-{ stdenv
-, lib
-, callPackage
-, mosdepth
-, index ? callPackage ./samtools-index.nix {}
-, flags ? null}:
+{ bionix
+, nixpkgs
+, indexAttrs ? {}
+, flags ? null
+}:
+with nixpkgs;
with lib;
input:
@@ -15,7 +15,7 @@ stdenv.mkDerivation {
buildCommand = ''
mkdir $out
ln -s ${input} input.bam
- ln -s ${index input} input.bam.bai
+ ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
'';
}
diff --git a/tools/mosdepth-plot.nix b/tools/mosdepth-plot.nix
index e6d2c7d..f15e099 100644
--- a/tools/mosdepth-plot.nix
+++ b/tools/mosdepth-plot.nix
@@ -1,9 +1,9 @@
-{ stdenv
-, lib
-, mosdepth
-, python
-, flags ? null}:
+{ bionix
+, nixpkgs
+, flags ? null
+}:
+with nixpkgs;
with lib;
{ inputs
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index 447e530..ff940a5 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -1,8 +1,8 @@
{ bionix, nixpkgs }:
-with nixpkgs;
+with bionix;
{
- depth = attrs: callPackage ./mosdepth-depth.nix attrs;
- plot = attrs: callPackage ./mosdepth-plot.nix attrs;
+ depth = callBionix ./mosdepth-depth.nix;
+ plot = callBionix ./mosdepth-plot.nix;
}
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index 3e150d2..c0204dc 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -1,10 +1,8 @@
-{ stdenv
-, callPackage
-, lib
-, platypus
+{ bionix
+, nixpkgs
, ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
, flags ? null
}:
@@ -19,9 +17,9 @@ in stdenv.mkDerivation {
buildInputs = [ platypus ];
buildCommand = ''
ln -s ${ref} ref.fa
- ln -s ${index ref} ref.fa.fai
+ ln -s ${bionix.samtools.faix indexAttrs ref} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
- ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs}
+ ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
ls -l
platypus callVariants \
--nCPU=$NIX_BUILD_CORES \
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index a399857..72116b8 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -1,12 +1,11 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
, flags ? null
}:
input:
+with nixpkgs;
with lib;
stdenv.mkDerivation {
diff --git a/tools/samtools-flagstat.nix b/tools/samtools-flagstat.nix
index 790eeb4..ae36c94 100644
--- a/tools/samtools-flagstat.nix
+++ b/tools/samtools-flagstat.nix
@@ -1,11 +1,10 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
}:
input:
+with nixpkgs;
with lib;
stdenv.mkDerivation {
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index 2fd066f..4e09dc7 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -1,12 +1,11 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
, flags ? null
}:
input:
+with nixpkgs;
with lib;
stdenv.mkDerivation {
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index 1a79c9f..2de579e 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -1,13 +1,12 @@
-{ stdenv
-, callPackage
-, lib
-, samtools
+{ bionix
+, nixpkgs
, nameSort ? false
, flags ? null
}:
input:
+with nixpkgs;
with lib;
stdenv.mkDerivation {
diff --git a/tools/samtools.nix b/tools/samtools.nix
index 77e3815..6b08c6e 100644
--- a/tools/samtools.nix
+++ b/tools/samtools.nix
@@ -1,10 +1,10 @@
{ bionix, nixpkgs }:
-with nixpkgs;
+with bionix;
{
- faidx = attrs: callPackage ./samtools-faidx.nix attrs;
- flagstat = attrs: callPackage ./samtools-flagstat.nix attrs;
- index = attrs: callPackage ./samtools-index.nix attrs;
- sort = attrs: callPackage ./samtools-sort.nix attrs;
+ faidx = callBionix ./samtools-faidx.nix;
+ flagstat = callBionix ./samtools-flagstat.nix;
+ index = callBionix ./samtools-index.nix;
+ sort = callBionix ./samtools-sort.nix;
}
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index ec7a764..e7fbb58 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -1,15 +1,14 @@
-{ stdenv
-, callPackage
-, lib
-, strelka
+{ bionix
+, nixpkgs
, ref
-, index ? callPackage ./samtools-faidx.nix {}
-, bamIndex ? callPackage ./samtools-index.nix {}
+, indexAttrs ? {}
+, bamIndexAttrs ? {}
, flags ? null
}:
{normal, tumour}:
+with nixpkgs;
with lib;
let
@@ -21,9 +20,9 @@ in stdenv.mkDerivation {
buildInputs = [ strelka ];
buildCommand = ''
ln -s ${ref} ref.fa
- ln -s ${index ref} ref.fa.fai
+ ln -s ${bionix.samtools.faidx indexAttrs ref} ref.fa.fai
${concatMapStringsSep "\n" (p: "ln -s ${p} ${filename p}.bam") inputs}
- ${concatMapStringsSep "\n" (p: "ln -s ${bamIndex p} ${filename p}.bai") inputs}
+ ${concatMapStringsSep "\n" (p: "ln -s ${bionix.samtools.index bamIndexAttrs p} ${filename p}.bai") inputs}
configureStrelkaSomaticWorkflow.py \
--normalBam ${filename normal}.bam \
diff --git a/tools/strelka.nix b/tools/strelka.nix
index a115740..767c270 100644
--- a/tools/strelka.nix
+++ b/tools/strelka.nix
@@ -1,7 +1,7 @@
{ bionix, nixpkgs }:
-with nixpkgs;
+with bionix;
{
- call = attrs: callPackage ./strelka-call.nix attrs;
+ call = callBionix ./strelka-call.nix;
}