From 24ee2349c16f159f2627665938fd76d599055a9a Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 22 Nov 2018 10:43:54 +1100
Subject: gridss: fix configure file optional string error

---
 tools/gridss-identifyVariants.nix | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'tools/gridss-identifyVariants.nix')

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/
 
-- 
cgit v1.2.3


From 0ade062d2da8a7111b14aa3d72ef7c741e98352d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 22 Nov 2018 10:44:31 +1100
Subject: gridss: restructure gridss pipeline

---
 tools/gridss-identifyVariants.nix | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

(limited to 'tools/gridss-identifyVariants.nix')

diff --git a/tools/gridss-identifyVariants.nix b/tools/gridss-identifyVariants.nix
index c91de00..d37e7ae 100644
--- a/tools/gridss-identifyVariants.nix
+++ b/tools/gridss-identifyVariants.nix
@@ -2,8 +2,8 @@
 , nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
+, indexAttrs ? {}
 , assemblyAttrs ? {}
-, extractSVReadsAttrs ? {}
 , collectMetricsAttrs ? {}
 , softClipsToSplitReadsAttrs ? {}
 , flags ? null
@@ -34,6 +34,16 @@ let
     done
   '';
 
+  linkSV = input: ''
+    BASENAME=$(basename ${input})
+    WRKDIR="''${BASENAME}.gridss.working"
+    if [[ ! -e $WRKDIR ]] ; then
+      mkdir $WRKDIR
+    fi
+    ln -s ${input} $WRKDIR/$BASENAME.sv.bam
+    ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
+  '';
+
   assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs)));
 in
 
-- 
cgit v1.2.3