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authorl-d-s <l@sdf.org>2018-11-15 16:37:30 +1100
committerl-d-s <l@sdf.org>2018-11-15 16:37:30 +1100
commit121202685860545b1a0ddc0266452af5eeb83ce0 (patch)
tree1c2e2690a905eb0580cc42f02d77529a7c773522 /tools
parent5ad075658eea3d783bac013aae476dd22a371e71 (diff)
Need to test config != null
Diffstat (limited to 'tools')
-rw-r--r--tools/gridss-annotateVariants.nix2
-rw-r--r--tools/gridss-assemble.nix1
-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, 8 deletions
diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 33992c4..4422cd6 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
TMP_DIR=$TMPDIR/
mv out.vcf $out
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index cdda748..b6f4ffd 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -51,6 +51,7 @@ stdenv.mkDerivation rec {
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
WORKER_THREADS=$NIX_BUILD_CORES \
OUTPUT=$out \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/
'';
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index dc978fa..9afaf65 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
WORKER_THREADS=$NIX_BUILD_CORES \
TMP_DIR=. \
WORKING_DIR=. \
- ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("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 86732b8..8f87b6f 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=input.bam \
O=$out \
THRESHOLD_COVERAGE=${toString thresholdCoverage}
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index c1909f1..38bacc6 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=${input}\
O=$out/input \
AS=true \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index 5b19a3a..ebcc5b8 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
REFERENCE_SEQUENCE=ref.fa \
WORKING_DIR=$TMP_DIR \
TMP_DIR=$TMP_DIR \
- ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
I=${input} \
O=$out \
AS=true
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index e3ed1cc..b920f5f 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -36,7 +36,7 @@ stdenv.mkDerivation rec {
METRICS_OUTPUT=$out/input.sv_metrics \
INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
- ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
MIN_CLIP_LENGTH=${toString minClipLength}
'';
}
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index 16982e2..87d418b 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 ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 5fce894..c04b039 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -34,7 +34,7 @@ stdenv.mkDerivation rec {
I=${input} \
O=$out \
${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
- ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+ ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {}; }