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-rw-r--r--tools/gridss-annotateVariants.nix2
-rw-r--r--tools/gridss-assemble.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.nix4
-rw-r--r--tools/gridss-extractSVReads.nix2
-rw-r--r--tools/gridss-identifyVariants.nix2
-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
10 files changed, 11 insertions, 11 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 4422cd6..6c8fbc6 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -65,7 +65,7 @@ stdenv.mkDerivation rec {
INPUT_VCF=input.vcf \
OUTPUT_VCF=out.vcf \
WORKING_DIR=$TMPDIR/ \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.ggridssConfig config)} \
TMP_DIR=$TMPDIR/
mv out.vcf $out
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index b6f4ffd..1e25731 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -51,7 +51,7 @@ stdenv.mkDerivation rec {
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
WORKER_THREADS=$NIX_BUILD_CORES \
OUTPUT=$out \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/
'';
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 9afaf65..76adc74 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
WORKER_THREADS=$NIX_BUILD_CORES \
TMP_DIR=. \
WORKING_DIR=. \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.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 8f87b6f..3babab4 100644
--- a/tools/gridss-collectGridssMetrics.nix
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
java -Xmx1G -cp ${bionix.gridss.jar} \
gridss.analysis.CollectGridssMetrics \
${optionalString sorted "ASSUME_SORTED=true"} \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
I=input.bam \
O=$out \
THRESHOLD_COVERAGE=${toString thresholdCoverage}
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 38bacc6..ff6eb1f 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
mkdir $out
java -Xmx1G -cp ${bionix.gridss.jar} \
gridss.analysis.CollectGridssMetrics \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
I=${input}\
O=$out/input \
AS=true \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index ebcc5b8..f4f1617 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
REFERENCE_SEQUENCE=ref.fa \
WORKING_DIR=$TMP_DIR \
TMP_DIR=$TMP_DIR \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
I=${input} \
O=$out \
AS=true
diff --git a/tools/gridss-configFile.nix b/tools/gridss-configFile.nix
index 838c292..15eba55 100644
--- a/tools/gridss-configFile.nix
+++ b/tools/gridss-configFile.nix
@@ -27,10 +27,10 @@ let
builtins.head (
builtins.match "([0-9]+\.0?[1-9]*)0+" (builtins.toString attr)));
bool = name: attr: name + " = " + (if attr == true then "true" else "false");
- attrs = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr;
+ set = name: attr: attrsToGridssConfigStringPrepend (name + ".") attr;
# Allows for repeated fields (e.g. for adapters):
list = name: attr: concatStringsSep "\n" (map (x: iniLine name x) attr);
};
in configAttrs: (writeText
"gridss.properties.override"
- (attrsToGridssConfigString configAttrs))
+ ((attrsToGridssConfigString configAttrs) + "\n"))
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index b920f5f..54edc85 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
METRICS_OUTPUT=$out/input.sv_metrics \
INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
MIN_CLIP_LENGTH=${toString minClipLength}
'';
}
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index 87d418b..a53fcb7 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -61,7 +61,7 @@ stdenv.mkDerivation rec {
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
ASSEMBLY=${assembly} \
OUTPUT_VCF=out.vcf \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 40fa216..47a3abd 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
I=${input} \
O=$out \
${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
- ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-27 09:29:15 +0000