From e7e2eea4db02fcfab484c63f8ef86c7bfc810c4c Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Fri, 15 Mar 2019 11:13:39 +1100 Subject: add multicore passthru flag --- tools/ascat-callCNV.nix | 1 + tools/ascat-gccorrect.nix | 1 + tools/bowtie-align.nix | 1 + tools/bowtie-index.nix | 1 + tools/bwa-mem.nix | 1 + tools/cnvkit-batch.nix | 1 + tools/gridss-assemble.nix | 1 + tools/gridss-callVariants.nix | 1 + tools/gridss-softClipsToSplitReads.nix | 1 + tools/kallisto-quant.nix | 1 + tools/mosdepth-depth.nix | 1 + tools/platypus-callVariants.nix | 1 + tools/samtools-flagstat.nix | 1 + tools/samtools-index.nix | 1 + tools/samtools-sort.nix | 1 + tools/strelka-call.nix | 1 + tools/strelka-callSomatic.nix | 1 + 17 files changed, 17 insertions(+) (limited to 'tools') 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; } -- cgit v1.2.3