From f3dc7987e0e841b97fd43160c68f8d09265083bc Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 2 Sep 2020 14:57:01 +1000
Subject: gridss: add missing flags parameter

---
 tools/gridss-assemble.nix              | 3 ++-
 tools/gridss-collectMetrics.nix        | 9 +++++----
 tools/gridss-extractSVReads.nix        | 3 ++-
 tools/gridss-softClipsToSplitReads.nix | 9 +++++----
 tools/gridss-variants.nix              | 3 +--
 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 \
-- 
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