From 9cf1724895f001c625fba37d78f517acb6938e07 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 2 Sep 2020 16:24:37 +1000
Subject: gridss: shard assembly into 10 pieces by default

---
 tools/gridss-assemble.nix | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

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

diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index a532f4b..f0a2693 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -6,6 +6,9 @@
 , flags ? null
 , config ? null
 , heapSize ? "31g"
+, workdirs ? []
+, jobIndex ? null
+, jobNodes ? null
 }:
 
 with bionix;
@@ -37,7 +40,8 @@ assert (homoRef);
 
 stage rec {
   name = "gridss-assemble";
-  buildInputs = with pkgs; [ jre bwa ];
+  buildInputs = with pkgs; [ jre bwa rsync ];
+  outputs = [ "out" "work" ];
   buildCommand = ''
     TMPDIR=$(pwd)
     ln -s ${ref} ref.fa
@@ -46,7 +50,8 @@ stage rec {
       ln -s $f
     done
     ${concatMapStringsSep "\n" linkInput inputs}
-	  java -Xmx${heapSize} -Dsamjdk.create_index=true \
+    ${concatMapStringsSep "\n" (w: "rsync -a --ignore-existing ${w}/ ./") workdirs}
+    java -Xmx${heapSize} -Dsamjdk.create_index=true \
       -cp ${bionix.gridss.jar} gridss.AssembleBreakends \
       VERBOSITY=WARNING \
       REFERENCE_SEQUENCE=ref.fa \
@@ -56,7 +61,13 @@ stage rec {
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/ \
+      ${optionalString (jobIndex != null) "JOB_INDEX=${toString jobIndex}"} \
+      ${optionalString (jobIndex != null) "JOB_NODES=${toString jobNodes}"} \
       ${optionalString (flags != null) flags}
+    rm -rf tmp
+    touch $out
+    cp -r $TMPDIR $work
+    chmod u+rwX -R $work
   '';
   passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
   passthru.multicore = true;
-- 
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