Fix up gridss config file.

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 {}; };