diff options
Diffstat (limited to 'tools/gridss-variants.nix')
| -rw-r--r-- | tools/gridss-variants.nix | 49 |
1 files changed, 29 insertions, 20 deletions
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; }; }; |