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-rwxr-xr-xlib/references.nix22
-rw-r--r--tools/gridss-softClipsToSplitReads.nix8
-rw-r--r--tools/gridss.nix4
3 files changed, 26 insertions, 8 deletions
diff --git a/lib/references.nix b/lib/references.nix
index bdeefa6..1ac92de 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -82,6 +82,28 @@ rec {
buildCommand = "gunzip < $src > $out";
passthru.filetype = filetype.fa {};
};
+ ensembl = {
+ cdna = stdenvNoCC.mkDerivation rec {
+ name = "ensembl-grch38-cdna-${version}";
+ version = "94";
+ src = fetchurl {
+ url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz";
+ sha256 = "0khp9l6s35lav2xqp7vkk6ybnz4wjihn7lapjf2lbpnbzjb4hp6d";
+ };
+ buildCommand = "gunzip < $src > $out";
+ passthru.filetype = filetype.fa {};
+ };
+ ncrna = stdenvNoCC.mkDerivation rec {
+ name = "ensembl-grch38-ncrna-${version}";
+ version = "94";
+ src = fetchurl {
+ url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/mus_musculus/ncrna/Mus_musculus.GRCm38.ncrna.fa.gz";
+ sha256 = "0d997gm8p2b89rm5d46m2x4vz9lijxarfr2lzylnbi8gyqrbagdd";
+ };
+ buildCommand = "gunzip < $src > $out";
+ passthru.filetype = filetype.fa {};
+ };
+ };
};
mm10 = mm10-p4;
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 35cd7b4..5fce894 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -21,7 +21,7 @@ assert (matchFileSorting "gridss-softClipsToSplitReads" { name = _: true; } inpu
stdenv.mkDerivation rec {
name = "gridss-softClipsToSplitReads";
- buildInputs = [ jre ];
+ buildInputs = [ jre bwa ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
@@ -37,9 +37,5 @@ stdenv.mkDerivation rec {
${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
- passthru.filetype =
- if alignerStreaming then
- filetype.bam { ref = ref; sort = sorting.none {}; }
- else
- input.filetype;
+ passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; }
}
diff --git a/tools/gridss.nix b/tools/gridss.nix
index bc2f0b8..1e4e2d1 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -17,6 +17,6 @@ rec {
assemble = callBionix ./gridss-assemble.nix;
identifyVariants = callBionix ./gridss-identifyVariants.nix;
annotateVariants = callBionix ./gridss-annotateVariants.nix;
- preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input)))));
- call = inputs: annotateVariants {} (map preprocessBam inputs);
+ preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input)))));
+ call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs);
}