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-annotateVariants.nix | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

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

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 4422cd6..cae5daf 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -2,8 +2,8 @@
 , nixpkgs
 , bwaIndexAttrs ? {}
 , faidxAttrs ? {}
+, indexAttrs ? {}
 , assemblyAttrs ? {}
-, extractSVReadsAttrs ? {}
 , collectMetricsAttrs ? {}
 , softClipsToSplitReadsAttrs ? {}
 , identifyVariantsAttrs ? {}
@@ -35,6 +35,16 @@ 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
 
@@ -50,12 +60,10 @@ stdenv.mkDerivation rec {
     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
     ln -s ${identifyVariants identifyVariantsAttrs inputs} input.vcf
 	  java -Xmx4g -Dsamjdk.create_index=true \
       -cp ${jar} gridss.AnnotateVariants \
-- 
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