Correct argument for gridss option file

9 files changed, 9 insertions, 9 deletions

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index adc4958..655b268 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -73,7 +73,7 @@ stdenv.mkDerivation rec {
       INPUT_VCF=input.vcf \
       OUTPUT_VCF=out.vcf \
       WORKING_DIR=$TMPDIR/ \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" +  bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" +  bionix.gridss.gridssConfig config)} \
       TMP_DIR=$TMPDIR/
 
     mv out.vcf $out
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index b61f28a..847830a 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=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/
   '';
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 76adc74..48f7cb2 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
       WORKER_THREADS=$NIX_BUILD_CORES \
 	    TMP_DIR=. \
 	    WORKING_DIR=. \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_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 3babab4..91e04c7 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=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			I=input.bam \
 			O=$out \
 			THRESHOLD_COVERAGE=${toString thresholdCoverage}
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index ff6eb1f..b68aeb1 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=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			I=${input}\
 			O=$out/input \
       AS=true \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index f4f1617..9267809 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
 			REFERENCE_SEQUENCE=ref.fa \
 			WORKING_DIR=$TMP_DIR \
 			TMP_DIR=$TMP_DIR \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			I=${input} \
 			O=$out \
       AS=true
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index b50a01c..5fc4c59 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -37,7 +37,7 @@ stdenv.mkDerivation rec {
       I=input.bam \
       O=$out \
       UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
       MIN_CLIP_LENGTH=${toString minClipLength}
   '';
   passthru.filetype = input.filetype;
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index d2dc665..23a9d85 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -69,7 +69,7 @@ stdenv.mkDerivation rec {
       ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
       ASSEMBLY=${assembly} \
       OUTPUT_VCF=out.vcf \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/
 
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 2fff15c..9bce063 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -32,7 +32,7 @@ stdenv.mkDerivation rec {
 			I=${input} \
 			O=$out \
       ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
-      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
+      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
   passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;};