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-rw-r--r--default.nix1
-rwxr-xr-xlib/references.nix22
-rw-r--r--lib/types.nix3
-rw-r--r--tools/bwa-mem.nix2
-rw-r--r--tools/gridss-annotateVariants.nix2
-rw-r--r--tools/gridss-callVariants.nix2
-rw-r--r--tools/gridss-collectGridssMetrics.nix2
-rw-r--r--tools/gridss-collectMetrics.nix2
-rw-r--r--tools/gridss-computeSamTags.nix2
-rw-r--r--tools/gridss-configFile.nix36
-rw-r--r--tools/gridss-extractSVReads.nix2
-rw-r--r--tools/gridss-identifyVariants.nix2
-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
-rw-r--r--tools/gridss.nix1
-rw-r--r--tools/kallisto-index.nix22
-rw-r--r--tools/kallisto-quant.nix48
-rw-r--r--tools/kallisto.nix8
-rw-r--r--tools/samtools-sort.nix17
18 files changed, 170 insertions, 6 deletions
diff --git a/default.nix b/default.nix
index 5218a99..f835fa0 100644
--- a/default.nix
+++ b/default.nix
@@ -15,6 +15,7 @@ let
fastqc = callBionix ./tools/fastqc.nix {};
gridss = callBionix ./tools/gridss.nix {};
infercnv = callBionix ./tools/infercnv.nix {};
+ kallisto = callBionix ./tools/kallisto.nix {};
mosdepth = callBionix ./tools/mosdepth.nix {};
mutect = callBionix ./tools/mutect.nix {};
platypus = callBionix ./tools/platypus.nix {};
diff --git a/lib/references.nix b/lib/references.nix
index 498cfd9..bdeefa6 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -46,6 +46,28 @@ rec {
'';
passthru.filetype = filetype.vcf { ref = seq; };
};
+ ensembl = {
+ cdna = stdenvNoCC.mkDerivation rec {
+ name = "ensembl-grch38-cdna-${version}";
+ version = "94";
+ src = fetchurl {
+ url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
+ sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h";
+ };
+ 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/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+ sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff";
+ };
+ buildCommand = "gunzip < $src > $out";
+ passthru.filetype = filetype.fa {};
+ };
+ };
};
grcm38 = grcm38-p6;
diff --git a/lib/types.nix b/lib/types.nix
index 4dbc6ff..ef9b1b7 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -21,7 +21,8 @@ let
in
rec {
- matchFiletype = sym: y: x: if x ? filetype then match x.filetype (defError (idft sym) y filetype) else abort "unknown filetype for ${sym}";
+ matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}";
+ matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype);
filetype = make-type "filetype" {
fa = {};
fq = {};
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 3420294..2b3bc64 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -17,7 +17,7 @@ with bionix.compression;
let
fa = f: matchFiletype "bwa-ref" { fa = _: f; } f;
- fq = f: matchFiletype "bwa-input" { fq = _: f; } f;
+ fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f;
in stdenv.mkDerivation {
name = "bwa-mem";
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 4f66c6c..33992c4 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -8,6 +8,7 @@
, softClipsToSplitReadsAttrs ? {}
, identifyVariantsAttrs ? {}
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -64,6 +65,7 @@ stdenv.mkDerivation rec {
INPUT_VCF=input.vcf \
OUTPUT_VCF=out.vcf \
WORKING_DIR=$TMPDIR/ \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
TMP_DIR=$TMPDIR/
mv out.vcf $out
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 416eb7c..dc978fa 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -4,6 +4,7 @@
, bwaIndexAttrs ? {}
, faidxAttrs ? {}
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -41,6 +42,7 @@ stdenv.mkDerivation rec {
WORKER_THREADS=$NIX_BUILD_CORES \
TMP_DIR=. \
WORKING_DIR=. \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
REFERENCE_SEQUENCE="ref.fa" \
${concatMapStringsSep " " (i: "INPUT=\"${i}\"") inputs} \
OUTPUT="$out/gridss.vcf" \
diff --git a/tools/gridss-collectGridssMetrics.nix b/tools/gridss-collectGridssMetrics.nix
index bb8d2e9..86732b8 100644
--- a/tools/gridss-collectGridssMetrics.nix
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -2,6 +2,7 @@
, nixpkgs
, thresholdCoverage ? 10000
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -25,6 +26,7 @@ stdenv.mkDerivation rec {
java -Xmx1G -cp ${bionix.gridss.jar} \
gridss.analysis.CollectGridssMetrics \
${optionalString sorted "ASSUME_SORTED=true"} \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=input.bam \
O=$out \
THRESHOLD_COVERAGE=${toString thresholdCoverage}
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 4688808..c1909f1 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -2,6 +2,7 @@
, nixpkgs
, thresholdCoverage ? 10000
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -22,6 +23,7 @@ stdenv.mkDerivation rec {
mkdir $out
java -Xmx1G -cp ${bionix.gridss.jar} \
gridss.analysis.CollectGridssMetrics \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=${input}\
O=$out/input \
AS=true \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index f75cea0..5b19a3a 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -4,6 +4,7 @@
, bwaIndexAttrs ? {}
, faidxAttrs ? {}
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -34,6 +35,7 @@ stdenv.mkDerivation rec {
REFERENCE_SEQUENCE=ref.fa \
WORKING_DIR=$TMP_DIR \
TMP_DIR=$TMP_DIR \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=${input} \
O=$out \
AS=true
diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix
new file mode 100644
index 0000000..838c292
--- /dev/null
+++ b/tools/gridss-configFile.nix
@@ -0,0 +1,36 @@
+{bionix, nixpkgs}:
+
+with nixpkgs;
+
+let
+ attrsToGridssConfigString = attrsToGridssConfigStringPrepend "";
+
+ attrsToGridssConfigStringPrepend = prepend: attrs:
+ lib.concatStringsSep "\n" (
+ lib.attrValues (
+ lib.mapAttrs
+ (name: attr: prepend + (iniLine name attr))
+ attrs));
+
+ iniLine = name: attr:
+ let attrType = builtins.typeOf attr;
+ in
+ if (iniLineByAttrType ? ${attrType})
+ then (iniLineByAttrType.${attrType} name attr)
+ else builtins.throw (
+ "`gridssConfig` cannot convert attribute of type \"" + attrType + "\".");
+
+ iniLineByAttrType = {
+ string = name: attr: name + " = " + attr;
+ int = name: attr: name + " = " + builtins.toString attr;
+ float = name: attr: name + " = " + (
+ builtins.head (
+ builtins.match "([0-9]+\.0?[1-9]*)0+" (builtins.toString attr)));
+ bool = name: attr: name + " = " + (if attr == true then "true" else "false");
+ attrs = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr;
+ # Allows for repeated fields (e.g. for adapters):
+ list = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr);
+ };
+in configAttrs: (writeText
+ "gridss.properties.override"
+ (attrsToGridssConfigString configAttrs))
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index a10abf5..e3ed1cc 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -5,6 +5,7 @@
, flags ? null
, unmappedReads ? false
, minClipLength ? 5
+, config ? null
}:
with nixpkgs;
@@ -35,6 +36,7 @@ stdenv.mkDerivation rec {
METRICS_OUTPUT=$out/input.sv_metrics \
INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
MIN_CLIP_LENGTH=${toString minClipLength}
'';
}
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index f44771b..16982e2 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -7,6 +7,7 @@
, collectMetricsAttrs ? {}
, softClipsToSplitReadsAttrs ? {}
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -60,6 +61,7 @@ stdenv.mkDerivation rec {
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
ASSEMBLY=${assembly} \
OUTPUT_VCF=out.vcf \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index cc40e52..b35d41d 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -4,6 +4,7 @@
, faidxAttrs ? {}
, alignerStreaming ? false
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -33,6 +34,7 @@ stdenv.mkDerivation rec {
I=${input} \
O=$out \
${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
+ ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
passthru.filetype =
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 792d279..1e4e2d1 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -8,6 +8,7 @@ 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;
diff --git a/tools/kallisto-index.nix b/tools/kallisto-index.nix
new file mode 100644
index 0000000..33dfb80
--- /dev/null
+++ b/tools/kallisto-index.nix
@@ -0,0 +1,22 @@
+{bionix
+, nixpkgs
+, kmerSize ? 31
+, unique ? false}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (kmerSize > 1);
+
+input:
+
+assert (matchFiletype input { fa = _: true; } input);
+
+stdenv.mkDerivation {
+ name = "kallisto-index";
+ buildInputs = [ kallisto ];
+ buildCommand = ''
+ kallisto index -k ${toString kmerSize} ${optionalString unique "--make-unique"} -i $out ${input}
+ '';
+}
diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix
new file mode 100644
index 0000000..c410721
--- /dev/null
+++ b/tools/kallisto-quant.nix
@@ -0,0 +1,48 @@
+{bionix
+, nixpkgs
+, indexFlags ? {}
+, bias ? false
+, bootstrapSamples ? 0
+, seed ? 42
+, plaintext ? false
+, fusion ? false
+, single ? false
+, frStranded ? false
+, rfStranded ? false
+, fragmentLength ? null
+, fragmentSD ? null
+, ref}:
+
+with nixpkgs;
+with lib;
+
+assert (!single || (fragmentLength != null && fragmentSD != null));
+
+inputs:
+
+let
+ inherit (bionix.types) matchFiletype';
+ isFastQ = matchFiletype' "kallisto-quant" {fq = _: true; gz = isFastQ; };
+in
+
+assert (all (x: isFastQ (x.filetype)) inputs);
+
+stdenv.mkDerivation {
+ name = "kallisto-quant";
+ buildInputs = [ kallisto ];
+ buildCommand = ''
+ mkdir $out
+ kallisto quant \
+ -i ${bionix.kallisto.index indexFlags ref} \
+ -o $out \
+ ${optionalString bias "--bias"} \
+ ${optionalString (bootstrapSamples > 0) "-b ${toString bootstrapSamples} --seed=${toString seed}"} \
+ ${optionalString plaintext "--plaintext"} \
+ ${optionalString fusion "--fusion"} \
+ ${optionalString single "--single -l ${toString fragmentLength} -s ${toString fragmentSD}"} \
+ ${optionalString frStranded "--fr-stranded"} \
+ ${optionalString rfStranded "--rf-stranded"} \
+ -t $NIX_BUILD_CORES \
+ ${concatStringsSep " " inputs}
+ '';
+}
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
new file mode 100644
index 0000000..f13f493
--- /dev/null
+++ b/tools/kallisto.nix
@@ -0,0 +1,8 @@
+{bionix, nixpkgs}:
+
+with bionix;
+
+{
+ index = callBionix ./kallisto-index.nix;
+ quant = callBionix ./kallisto-quant.nix;
+}
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index ab9d603..5a02dab 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -11,7 +11,7 @@ with nixpkgs;
with lib;
let
- inherit (bionix.types) matchFiletype coordSort;
+ inherit (bionix.types) matchFiletype coordSort matchFileSorting;
in
assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _: true; } input);
@@ -19,11 +19,20 @@ assert (matchFiletype "samtools-sort" { bam = _: true; sam = _: true; cram = _:
let
outfmtR = if outfmt != null then outfmt input else input.filetype;
outFmtFlags = matchFiletype "samtools-sort-outfmt" { bam = _: "-O BAM"; sam = _: "-O SAM"; cram = ref: "-O CRAM -T ${ref}"; } {filetype = outfmtR;};
+ alreadySorted = matchFileSorting "samtools-sort" { name = _: nameSort; coord = _: !nameSort; } input;
in stdenv.mkDerivation {
name = "samtools-sort";
buildInputs = [ samtools ];
- buildCommand = ''
- samtools sort -@ $NIX_BUILD_CORES ${optionalString nameSort "-n"} ${outFmtFlags} ${optionalString (flags != null) flags} ${input} > $out
- '';
+ buildCommand =
+ if alreadySorted then
+ "ln -s $out ${input}"
+ else
+ ''
+ samtools sort -@ $NIX_BUILD_CORES \
+ ${optionalString nameSort "-n"} \
+ ${outFmtFlags} \
+ ${optionalString (flags != null) flags} \
+ ${input} > $out
+ '';
passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
}
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-28 00:46:41 +0000