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authorJustin Bedo <cu@cua0.org>2020-09-02 14:57:01 +1000
committerJustin Bedo <cu@cua0.org>2020-09-02 14:57:01 +1000
commitf3dc7987e0e841b97fd43160c68f8d09265083bc (patch)
treee834d0eaa11ab00f9e18deb150d0511c0482dddb
parent2cee6ee61240fbbc7f9684208b67eae8634404bf (diff)
gridss: add missing flags parameter
-rw-r--r--tools/gridss-assemble.nix3
-rw-r--r--tools/gridss-collectMetrics.nix9
-rw-r--r--tools/gridss-extractSVReads.nix3
-rw-r--r--tools/gridss-softClipsToSplitReads.nix9
-rw-r--r--tools/gridss-variants.nix3
5 files changed, 15 insertions, 12 deletions
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 14f39c8..a532f4b 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -55,7 +55,8 @@ stage rec {
OUTPUT=$out \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
- TMP_DIR=$TMPDIR/
+ TMP_DIR=$TMPDIR/ \
+ ${optionalString (flags != null) flags}
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
passthru.multicore = true;
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 2e3b3a9..8b09886 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -22,13 +22,14 @@ stage rec {
buildCommand = ''
mkdir $out
java -Xmx${heapSize} -cp ${bionix.gridss.jar} \
- gridss.analysis.CollectGridssMetrics \
+ gridss.analysis.CollectGridssMetrics \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
VERBOSITY=WARNING \
- I=${input}\
- O=$out/input \
+ I=${input}\
+ O=$out/input \
AS=true \
- THRESHOLD_COVERAGE=${toString thresholdCoverage}
+ THRESHOLD_COVERAGE=${toString thresholdCoverage} \
+ ${optionalString (flags != null) flags}
# Make the output deterministic by removing timestamps
sed -i '/^# Started on:/d' $out/input.*_metrics
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index cf9085d..6691808 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -38,7 +38,8 @@ stage rec {
O=$out \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
- MIN_CLIP_LENGTH=${toString minClipLength}
+ MIN_CLIP_LENGTH=${toString minClipLength} \
+ ${optionalString (flags != null) flags}
'';
passthru.filetype = input.filetype;
}
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index d480328..93d02df 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -30,12 +30,13 @@ stage rec {
java -Xmx${heapSize} -Dsamjdk.create_index=false \
-cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \
VERBOSITY=WARNING \
- REFERENCE_SEQUENCE=ref.fa \
- I=${input} \
- O=$out \
+ REFERENCE_SEQUENCE=ref.fa \
+ I=${input} \
+ O=$out \
${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
- WORKER_THREADS=$NIX_BUILD_CORES
+ WORKER_THREADS=$NIX_BUILD_CORES \
+ ${optionalString (flags != null) flags}
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
passthru.multicore = true;
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index 4f39b1e..ad4c66d 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -5,7 +5,6 @@
, assemblyAttrs ? {}
, collectMetricsAttrs ? {}
, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
-, flags ? null
, config ? null
, heapSize ? "4g"
}:
@@ -91,7 +90,7 @@ rec {
name = "gridss-annotateVariants";
buildInputs = with pkgs; [ jre ];
buildCommand = mkLinks + ''
- ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs flags config; } inputs} input.vcf
+ ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs config; } inputs} input.vcf
java -Xmx${heapSize} -Dsamjdk.create_index=true \
-cp ${jar} gridss.AnnotateVariants \
VERBOSITY=WARNING \