gridss: fix configure file optional string error

7 files changed, 16 insertions, 17 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 $out
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index dc978fa..9afaf65 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
       WORKER_THREADS=$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-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..b5ceffb 100644
--- a/tools/gridss-extractSVReads.nix
+++ b/tools/gridss-extractSVReads.nix
@@ -27,16 +27,17 @@ stdenv.mkDerivation rec {
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     ln -s ${bionix.samtools.dict dictIndexAttrs ref} ref.fa.dict
     ln -s ${input} input.bam
-    mkdir $out
+    for f in ${bionix.gridss.collectMetrics collectMetricsAttrs input}/* ; do
+      ln -s $f
+    done
     java -Dsamjdk.create_index=true \
       -cp ${bionix.gridss.jar} gridss.ExtractSVReads \
       REFERENCE_SEQUENCE=ref.fa \
       I=input.bam \
-      O=$out/input.sv.bam \
-      METRICS_OUTPUT=$out/input.sv_metrics \
-      INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
+      O=$out \
       UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
-      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+      ${optionalString (config != null) ("CONFIGURATION_FILE=" + gridssConfig config)} \
       MIN_CLIP_LENGTH=${toString minClipLength}
   '';
+  passthru.filetype = input.filetype;
 }
diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index 16982e2..c91de00 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -42,26 +42,24 @@ assert (homoRef);
 
 stdenv.mkDerivation rec {
   name = "gridss-identifyVariants";
-  buildInputs = [ jre ];
+  buildInputs = [ jre samtools ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
     for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
       ln -s $f
     done
-    ${concatMapStringsSep "\n" (linkInput extractSVReads extractSVReadsAttrs) inputs}
+    ${concatMapStringsSep "\n" (linkSV) inputs}
+    ${linkSV assembly}
     ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs}
     ${linkInput collectMetrics collectMetricsAttrs assembly}
-    ASSBASE=$(basename ${assembly})
-    ln -s ${assembly} $ASSBASE.gridss.working/$ASSBASE.sv.bam
-    ln -s ${bionix.samtools.index {} assembly} $ASSBASE.gridss.working/$ASSBASE.sv.bai
 	  java -Xmx4g -Dsamjdk.create_index=true \
       -cp ${jar} gridss.IdentifyVariants \
       REFERENCE_SEQUENCE=ref.fa \
       ${concatMapStringsSep " " (i: "INPUT='${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..1f9c8b4 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -34,8 +34,8 @@ stdenv.mkDerivation rec {
 			I=${input} \
 			O=$out \
       ${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
-      ${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
+      ${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
-  passthru.filetype = filetype.bam { ref = ref; sort = sorting.none {};  }
+  passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;};
 }