gridss: specify cores for all multithreaded phases

3 files changed, 87 insertions, 65 deletions

diff --git a/tools/gridss-computeSamTags.nix b/tools/gridss-computeSamTags.nix
index a2e1f8b..de44478 100644
--- a/tools/gridss-computeSamTags.nix
+++ b/tools/gridss-computeSamTags.nix
@@ -1,10 +1,5 @@
-{ bionix
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
-, flags ? null
-, config ? null
-, heapSize ? "1G"
-}:
+{ bionix, bwaIndexAttrs ? { }, faidxAttrs ? { }, flags ? null, config ? null
+, heapSize ? "1G" }:
 
 with bionix;
 with lib;
@@ -15,9 +10,8 @@ input:
 let
   ref = matchFiletype "gridss-computeSamTags" { bam = x: x.ref; } input;
   sorted = matchFileSorting "gridss-computeSamTags" { name = _: true; } input;
-in
 
-assert(sorted);
+in assert (sorted);
 
 stage rec {
   name = "gridss-computeSamTags";
@@ -30,15 +24,20 @@ stage rec {
     done
     java -Xmx${heapSize} \
       -Dsamjdk.create_index=false \
-			-cp ${bionix.gridss.jar} gridss.ComputeSamTags \
+      -cp ${bionix.gridss.jar} gridss.ComputeSamTags \
       VERBOSITY=WARNING \
-			REFERENCE_SEQUENCE=ref.fa \
-			WORKING_DIR=$TMP_DIR \
-			TMP_DIR=$TMP_DIR \
-      ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
-			I=${input} \
-			O=$out \
+      WORKER_THREADS=$NIX_BUILD_CORES \
+      REFERENCE_SEQUENCE=ref.fa \
+      WORKING_DIR=$TMP_DIR \
+      TMP_DIR=$TMP_DIR \
+      ${
+        optionalString (config != null)
+        ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)
+      } \
+      I=${input} \
+      O=$out \
       AS=true
   '';
   passthru.filetype = input.filetype;
+  passthru.multicore = true;
 }
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index c208758..a5c470a 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -1,14 +1,7 @@
-{ bionix
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
-, indexAttrs ? {}
-, assemblyAttrs ? {}
-, collectMetricsAttrs ? {}
+{ bionix, bwaIndexAttrs ? { }, faidxAttrs ? { }, indexAttrs ? { }
+, assemblyAttrs ? { }, collectMetricsAttrs ? { }
 , softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
-, config ? null
-, heapSize ? "4g"
-, shards ? 10
-}:
+, config ? null, heapSize ? "4g", shards ? 10 }:
 
 with bionix;
 with lib;
@@ -44,7 +37,9 @@ let
     ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
   '';
 
-  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.shardedAssemble shards assemblyAttrs inputs));
+  assembly = bionix.samtools.sort { }
+    (softClipsToSplitReads softClipsToSplitReadsAttrs
+      (bionix.gridss.shardedAssemble shards assemblyAttrs inputs));
 
   mkLinks = ''
     ln -s ${ref} ref.fa
@@ -54,13 +49,12 @@ let
     done
     ${concatMapStringsSep "\n" (linkSV) inputs}
     ${linkSV assembly}
-    ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs}
+    ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs)
+    inputs}
     ${linkInput collectMetrics collectMetricsAttrs assembly}
   '';
 
-in
-
-assert (all sorted inputs);
+in assert (all sorted inputs);
 assert (homoRef);
 
 rec {
@@ -74,16 +68,21 @@ rec {
         REFERENCE_SEQUENCE=ref.fa \
         ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
         ASSEMBLY=${assembly} \
+        WORKER_THREADS=$NIX_BUILD_CORES \
         OUTPUT_VCF=out.vcf \
-        ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
+        ${
+          optionalString (config != null)
+          ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)
+        } \
         WORKING_DIR=$TMPDIR/ \
         TMP_DIR=$TMPDIR/
 
       mv out.vcf $out
-      '';
+    '';
     passthru = {
       filetype = filetype.vcf { ref = ref; };
       gridss.assembly = assembly;
+      multicore = true;
     };
   };
 
@@ -91,7 +90,12 @@ rec {
     name = "gridss-annotateVariants";
     buildInputs = with pkgs; [ jre ];
     buildCommand = mkLinks + ''
-      ln -s ${bionix.gridss.identifyVariants {inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs collectMetricsAttrs softClipsToSplitReadsAttrs config; } inputs} input.vcf
+      ln -s ${
+        bionix.gridss.identifyVariants {
+          inherit bwaIndexAttrs faidxAttrs indexAttrs assemblyAttrs
+            collectMetricsAttrs softClipsToSplitReadsAttrs config;
+        } inputs
+      } input.vcf
       java -Xmx${heapSize} -Dsamjdk.create_index=true \
         -cp ${jar} gridss.AnnotateVariants \
         VERBOSITY=WARNING \
@@ -100,15 +104,20 @@ rec {
         ASSEMBLY=${assembly} \
         INPUT_VCF=input.vcf \
         OUTPUT_VCF=out.vcf \
+        WORKER_THREADS=$NIX_BUILD_CORES \
         WORKING_DIR=$TMPDIR/ \
-        ${optionalString (config != null) ("OPTIONS_FILE=" +  bionix.gridss.gridssConfig config)} \
+        ${
+          optionalString (config != null)
+          ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)
+        } \
         TMP_DIR=$TMPDIR/
 
       mv out.vcf $out
-      '';
+    '';
     passthru = {
       filetype = filetype.vcf { ref = ref; };
       gridss.assembly = assembly;
+      multicore = true;
     };
   };
 
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 70ba21d..a002e69 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -1,81 +1,95 @@
-{bionix}:
+{ bionix }:
 
 with bionix;
 with lib;
 
 rec {
   jar = pkgs.fetchurl {
-    url = "https://github.com/PapenfussLab/gridss/releases/download/v2.12.1/gridss-2.12.1-gridss-jar-with-dependencies.jar";
+    url =
+      "https://github.com/PapenfussLab/gridss/releases/download/v2.12.1/gridss-2.12.1-gridss-jar-with-dependencies.jar";
     sha256 = "sha256-wH5O+vYKlWGDJTTnMgKYrSNtzoU7wDHqNraiW8xrxXA=";
   };
 
   /* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format.
-  Type: genConfig :: attrSet -> ini file
+     Type: genConfig :: attrSet -> ini file
   */
-  genConfig = callBionix ./gridss-configFile.nix {};
+  genConfig = callBionix ./gridss-configFile.nix { };
 
   /* Invoke the callVariants tool
-  Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
+     Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants
   */
   callVariants = callBionixE ./gridss-callVariants.nix;
 
   /* Invoke computeSamTags tool
-  Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
+     Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam
   */
   computeSamTags = callBionixE ./gridss-computeSamTags.nix;
 
   /* Invoke softClipsToSplitReads tool
-  Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
+     Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam
   */
   softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix;
 
   /* Invoke collectMetrics tool
-  Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
+     Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics
   */
   collectMetrics = callBionixE ./gridss-collectMetrics.nix;
 
   /* Invoke extractSVReads tool
-  Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
+     Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam
   */
   extractSVReads = callBionixE ./gridss-extractSVReads.nix;
 
   /* Invoke assembly tool
-  Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
+     Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam
   */
   assemble = callBionixE ./gridss-assemble.nix;
   shardedAssemble = n: a: input:
-    let assemblies = genList (i: bionix.gridss.assemble (a // { jobNodes = n; jobIndex = i;}) input) n;
-    in if n <= 1 then bionix.gridss.assemble a input else bionix.gridss.assemble (a // {workdirs = map (a: a.work) assemblies;}) input;
+    let
+      assemblies = genList (i:
+        bionix.gridss.assemble (a // {
+          jobNodes = n;
+          jobIndex = i;
+        }) input) n;
+    in if n <= 1 then
+      bionix.gridss.assemble a input
+    else
+      bionix.gridss.assemble (a // { workdirs = map (a: a.work) assemblies; })
+      input;
 
   /* Invoke identifyVariants tool
-  Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+     Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
   */
-  identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
+  identifyVariants = exec
+    (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify);
 
   /* Invoke annotateVariants tool
-  Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
+     Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF
   */
-  annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
+  annotateVariants = exec
+    (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
 
-  /* As annotateVariants except include assembly in output */
-  annotateAndAssemble = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
+  # As annotateVariants except include assembly in output
+  annotateAndAssemble = exec (attrs: input:
+    ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
 
-  /* Preprocess BAM files to extract SV reads and compute required stats
-  Type: preprocessBam :: bam -> bam
+  /* Preprocess BAM files to extract SV reads
+     Type: preprocessBam :: bam -> bam
   */
   preprocessBam = with samtools;
     flip pipe [
-      (gridss.extractSVReads {})
-      (sort {nameSort = true;})
-      (gridss.computeSamTags {})
-      (sort {})
+      (gridss.extractSVReads { })
+      (sort { nameSort = true; })
+      (gridss.computeSamTags { })
+      (sort { })
     ];
 
-  /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual tools above.
-  Type: call :: [bam] -> GRIDSS result
+  /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools.
+     Type: [bam] -> GRIDSS result
   */
-  call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
+  call = inputs: gridss.annotateVariants { } (map gridss.preprocessBam inputs);
 
-  /* As call but include assemblies in output */
-  callAndAssemble = inputs: gridss.annotateAndAssemble {} (map gridss.preprocessBam inputs);
+  # As call but include assemblies in output
+  callAndAssemble = inputs:
+    gridss.annotateAndAssemble { } (map gridss.preprocessBam inputs);
 }