From 4574deb8e1649eaf63df424585d11645c7cfa7dd Mon Sep 17 00:00:00 2001
From: l-d-s <l@sdf.org>
Date: Mon, 12 Nov 2018 16:54:30 +1100
Subject: Attempt to integrate config file into GRIDSS stage

---
 tools/gridss-annotateVariants.nix      | 2 ++
 tools/gridss-callVariants.nix          | 2 ++
 tools/gridss-collectGridssMetrics.nix  | 2 ++
 tools/gridss-collectMetrics.nix        | 2 ++
 tools/gridss-computeSamTags.nix        | 2 ++
 tools/gridss-extractSVReads.nix        | 2 ++
 tools/gridss-identifyVariants.nix      | 2 ++
 tools/gridss-softClipsToSplitReads.nix | 2 ++
 tools/gridss.nix                       | 1 +
 9 files changed, 17 insertions(+)

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 4f66c6c..33992c4 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -8,6 +8,7 @@
 , softClipsToSplitReadsAttrs ? {}
 , identifyVariantsAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -64,6 +65,7 @@ stdenv.mkDerivation rec {
       INPUT_VCF=input.vcf \
       OUTPUT_VCF=out.vcf \
       WORKING_DIR=$TMPDIR/ \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
       TMP_DIR=$TMPDIR/
 
     mv out.vcf $out
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 416eb7c..dc978fa 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -4,6 +4,7 @@
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -41,6 +42,7 @@ stdenv.mkDerivation rec {
       WORKER_THREADS=$NIX_BUILD_CORES \
 	    TMP_DIR=. \
 	    WORKING_DIR=. \
+      ${optionalString config ("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 bb8d2e9..86732b8 100644
--- a/tools/gridss-collectGridssMetrics.nix
+++ b/tools/gridss-collectGridssMetrics.nix
@@ -2,6 +2,7 @@
 , nixpkgs
 , thresholdCoverage ? 10000
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -25,6 +26,7 @@ stdenv.mkDerivation rec {
     java -Xmx1G -cp ${bionix.gridss.jar} \
 			gridss.analysis.CollectGridssMetrics \
 			${optionalString sorted "ASSUME_SORTED=true"} \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			I=input.bam \
 			O=$out \
 			THRESHOLD_COVERAGE=${toString thresholdCoverage}
diff --git a/tools/gridss-collectMetrics.nix b/tools/gridss-collectMetrics.nix
index 4688808..c1909f1 100644
--- a/tools/gridss-collectMetrics.nix
+++ b/tools/gridss-collectMetrics.nix
@@ -2,6 +2,7 @@
 , nixpkgs
 , thresholdCoverage ? 10000
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -22,6 +23,7 @@ stdenv.mkDerivation rec {
     mkdir $out
     java -Xmx1G -cp ${bionix.gridss.jar} \
 			gridss.analysis.CollectGridssMetrics \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			I=${input}\
 			O=$out/input \
       AS=true \
diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index f75cea0..5b19a3a 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -4,6 +4,7 @@
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -34,6 +35,7 @@ stdenv.mkDerivation rec {
 			REFERENCE_SEQUENCE=ref.fa \
 			WORKING_DIR=$TMP_DIR \
 			TMP_DIR=$TMP_DIR \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			I=${input} \
 			O=$out \
       AS=true
diff --git a/tools/gridss-extractSVReads.nix b/tools/gridss-extractSVReads.nix
index a10abf5..e3ed1cc 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -5,6 +5,7 @@
 , flags ? null
 , unmappedReads ? false
 , minClipLength ? 5
+, config ? null
 }:
 
 with nixpkgs;
@@ -35,6 +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"} \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
       MIN_CLIP_LENGTH=${toString minClipLength}
   '';
 }
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index f44771b..16982e2 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -7,6 +7,7 @@
 , collectMetricsAttrs ? {}
 , softClipsToSplitReadsAttrs ? {}
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -60,6 +61,7 @@ stdenv.mkDerivation rec {
       ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
       ASSEMBLY=${assembly} \
       OUTPUT_VCF=out.vcf \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/
 
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 8a7dca3..35cd7b4 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -4,6 +4,7 @@
 , faidxAttrs ? {}
 , alignerStreaming ? false
 , flags ? null
+, config ? null
 }:
 
 with nixpkgs;
@@ -33,6 +34,7 @@ stdenv.mkDerivation rec {
 			I=${input} \
 			O=$out \
       ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
+      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
   passthru.filetype =
diff --git a/tools/gridss.nix b/tools/gridss.nix
index d46a8ce..bc2f0b8 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -8,6 +8,7 @@ rec {
     url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
     sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
   };
+  gridssConfig = callBionix ./gridss-configFile.nix {};
   callVariants = callBionix ./gridss-callVariants.nix;
   computeSamTags = callBionix ./gridss-computeSamTags.nix;
   softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix;
-- 
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