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authorJustin Bedo <cu@cua0.org>2018-12-18 14:05:19 +1100
committerJustin Bedo <cu@cua0.org>2018-12-18 14:11:57 +1100
commit0418c23f5d3bff108744d96d1075b0e76b580fdd (patch)
tree4a77565abe39bba1dc93139f2d4539496a041198 /tools
parent2ec0e115917d194eeea6ef4c1b4b1f7f6a7f416b (diff)
qsub: refactor overriding
Diffstat (limited to 'tools')
-rw-r--r--tools/bowtie.nix4
-rw-r--r--tools/bwa.nix4
-rw-r--r--tools/fastqc.nix2
-rw-r--r--tools/gridss.nix18
-rw-r--r--tools/infercnv.nix2
-rw-r--r--tools/kallisto.nix4
-rw-r--r--tools/mosdepth.nix4
-rw-r--r--tools/mutect.nix2
-rw-r--r--tools/platypus.nix2
-rw-r--r--tools/samtools.nix18
-rw-r--r--tools/strelka.nix2
11 files changed, 31 insertions, 31 deletions
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;
}