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authorl-d-s <l@sdf.org>2018-11-12 16:54:30 +1100
committerl-d-s <l@sdf.org>2018-11-12 16:54:30 +1100
commit4574deb8e1649eaf63df424585d11645c7cfa7dd (patch)
tree165478a6535a1b0172f489c03eb2a6d8ac18c023
parentb46138826260f1ed963ffe18fef7ec4ce70b6de8 (diff)
Attempt to integrate config file into GRIDSS stage
-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-extractSVReads.nix2
-rw-r--r--tools/gridss-identifyVariants.nix2
-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
-rw-r--r--tools/gridss.nix1
9 files changed, 17 insertions, 0 deletions
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=$out \
AS=true
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index a10abf5..e3ed1cc 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -5,6 +5,7 @@
, flags ? null
, unmappedReads ? false
, minClipLength ? 5
+, config ? null
}:
with nixpkgs;
@@ -35,6 +36,7 @@ stdenv.mkDerivation rec {
METRICS_OUTPUT=$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=$TMPDIR/
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 8a7dca3..35cd7b4 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -4,6 +4,7 @@
, faidxAttrs ? {}
, alignerStreaming ? false
, flags ? null
+, config ? null
}:
with nixpkgs;
@@ -33,6 +34,7 @@ stdenv.mkDerivation rec {
I=${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 d46a8ce..bc2f0b8 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;