add multicore passthru flag

17 files changed, 17 insertions, 0 deletions

diff --git a/tools/ascat-callCNV.nix b/tools/ascat-callCNV.nix
index 357ab8a..f74bb18 100644
--- a/tools/ascat-callCNV.nix
+++ b/tools/ascat-callCNV.nix
@@ -34,4 +34,5 @@ stage rec {
       -protocol WGS \
       -cpus $NIX_BUILD_CORES
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/ascat-gccorrect.nix b/tools/ascat-gccorrect.nix
index c1838d9..584c2ae 100644
--- a/tools/ascat-gccorrect.nix
+++ b/tools/ascat-gccorrect.nix
@@ -33,4 +33,5 @@ stage rec {
       sed 1d $f >> $out
     done
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 67a1169..65d0e9f 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -32,4 +32,5 @@ in stage {
       > $out
   '';
   passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.multicore = true;
 }
diff --git a/tools/bowtie-index.nix b/tools/bowtie-index.nix
index 4554ad1..4607995 100644
--- a/tools/bowtie-index.nix
+++ b/tools/bowtie-index.nix
@@ -18,4 +18,5 @@ stage {
     mkdir $out
     bowtie2-build --seed ${toString seed} --threads $NIX_BUILD_CORES ${optionalString (flags != null) flags} ${ref} $out/ref
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 1427b49..e58ef03 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -36,4 +36,5 @@ in stage {
       > $out
   '';
   passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.multicore = true;
 }
diff --git a/tools/cnvkit-batch.nix b/tools/cnvkit-batch.nix
index 6fb97a4..d033dc4 100644
--- a/tools/cnvkit-batch.nix
+++ b/tools/cnvkit-batch.nix
@@ -37,4 +37,5 @@ stage {
     mkdir $out
     cp * $out
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index e5cb3ca..27bbe32 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -57,4 +57,5 @@ stage rec {
       TMP_DIR=$TMPDIR/
   '';
   passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
+  passthru.multicore = true;
 }
diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix
index 4117126..1ec9206 100644
--- a/tools/gridss-callVariants.nix
+++ b/tools/gridss-callVariants.nix
@@ -50,4 +50,5 @@ stage rec {
       ${optionalString (blacklist != null) ("BLACKLIST=" + blacklist)} \
       ${optionalString (flags != null) flags}
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 315fbf9..4a73e3c 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -37,4 +37,5 @@ stage rec {
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
   passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
+  passthru.multicore = true;
 }
diff --git a/tools/kallisto-quant.nix b/tools/kallisto-quant.nix
index 1deab67..9f0ab57 100644
--- a/tools/kallisto-quant.nix
+++ b/tools/kallisto-quant.nix
@@ -44,4 +44,5 @@ stage {
       -t $NIX_BUILD_CORES \
       ${concatStringsSep " " inputs}
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/mosdepth-depth.nix b/tools/mosdepth-depth.nix
index 448da11..2dbfc8d 100644
--- a/tools/mosdepth-depth.nix
+++ b/tools/mosdepth-depth.nix
@@ -17,4 +17,5 @@ stage {
     ln -s ${bionix.samtools.index indexAttrs input} input.bam.bai
     mosdepth -t $NIX_BUILD_CORES ${optionalString (flags != null) flags} $out/out input.bam
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/platypus-callVariants.nix b/tools/platypus-callVariants.nix
index a5e497e..f3b3e7c 100644
--- a/tools/platypus-callVariants.nix
+++ b/tools/platypus-callVariants.nix
@@ -37,4 +37,5 @@ stage {
       --bamFiles=${concatMapStringsSep "," (p: "${filename p}.bam") inputs}
   '';
   passthru.filetype = filetype.vcf {ref = ref;};
+  passthru.multicore = true;
 }
diff --git a/tools/samtools-flagstat.nix b/tools/samtools-flagstat.nix
index 57d8bb6..d733f2f 100644
--- a/tools/samtools-flagstat.nix
+++ b/tools/samtools-flagstat.nix
@@ -10,4 +10,5 @@ stage {
   name = "samtools-index";
   buildInputs = with pkgs; [ samtools ];
   buildCommand = "samtools flagstat -@ $NIX_BUILD_CORES ${input} > $out";
+  passthru.multicore = true;
 }
diff --git a/tools/samtools-index.nix b/tools/samtools-index.nix
index 84ebbe1..d0f8d7a 100644
--- a/tools/samtools-index.nix
+++ b/tools/samtools-index.nix
@@ -19,4 +19,5 @@ stage {
     samtools index -@ $NIX_BUILD_CORES ${optionalString (flags != null) flags} input.bam
     cp input.bam.bai $out
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/samtools-sort.nix b/tools/samtools-sort.nix
index d01c83f..e3fbff8 100644
--- a/tools/samtools-sort.nix
+++ b/tools/samtools-sort.nix
@@ -34,4 +34,5 @@ in stage {
           ${input} > $out
       '';
   passthru.filetype = if nameSort then bionix.types.nameSort outfmtR else coordSort outfmtR;
+  passthru.multicore = true;
 }
diff --git a/tools/strelka-call.nix b/tools/strelka-call.nix
index 1162558..4471d7d 100644
--- a/tools/strelka-call.nix
+++ b/tools/strelka-call.nix
@@ -40,4 +40,5 @@ stage {
 
     cp -r results $out
   '';
+  passthru.multicore = true;
 }
diff --git a/tools/strelka-callSomatic.nix b/tools/strelka-callSomatic.nix
index 5be4c0e..ed5626b 100644
--- a/tools/strelka-callSomatic.nix
+++ b/tools/strelka-callSomatic.nix
@@ -42,4 +42,5 @@ stage {
 
     cp -r results $out
   '';
+  passthru.multicore = true;
 }