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authorl-d-s <distefano.l@wehi.edu.au>2018-11-29 12:10:45 +1100
committerl-d-s <distefano.l@wehi.edu.au>2018-11-29 12:10:45 +1100
commit16951e6f99636a2c9d924d49c549a918e403f276 (patch)
tree677033f3d8edecfa238c39fc8d023ec9d1347f02 /tools
parentdcb23a997359160ffdc58a971027fd77c45c7157 (diff)
Correct argument for gridss option file
Diffstat (limited to 'tools')
-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-extractSVReads.nix2
-rw-r--r--tools/gridss-identifyVariants.nix2
-rw-r--r--tools/gridss-softClipsToSplitReads.nix2
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;};