[galaxy-commits] commit/galaxy-central: dan: GATK Updates.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/542cc69a4486/ changeset: 542cc69a4486 user: dan date: 2012-01-23 17:37:49 summary: GATK Updates. affected #: 7 files diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -9,7 +9,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -25,4 +25,4 @@ ##contig=<ID=phiX174,length=5386> ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf --- a/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf +++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -10,7 +10,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -28,4 +28,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf --- a/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf +++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.1 ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=from_variant_annotator source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/input_variant_from_variant_annotator.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=from_variant_annotator printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false" ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -11,7 +11,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -30,4 +30,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DP=10;MQ=37.74;MQ0=0;QD=0.00;set=ReferenceInAll GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DB;DP=10;MQ=37.74;MQ0=0;set=ReferenceInAll GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular --- a/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular +++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular @@ -1,36 +1,30 @@ ##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites -CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate -CompOverlap dbsnp input_0 none all 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp input_0 none known 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp input_0 none novel 0 0 0 0.00000000 0 0.00000000 +CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate +CompOverlap dbsnp input_0 none all 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none known 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none novel 0 0 0 0.00 0 0.00 ##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample -CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio -CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 - -##:GATKReport.v0.2 SimpleMetricsByAC.metrics : TiTv by allele count -SimpleMetricsByAC.metrics CompRod EvalRod JexlExpression Novelty row AC nTi nTv n TiTv -SimpleMetricsByAC.metrics dbsnp input_0 none all ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none all ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none all ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac2 2 0 0 0 0.0 +CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio +CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 ##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator -TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio -TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 +TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio +TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00 0 0 0.00 0 0 0.00 ##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay -ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites -ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00000000 NaN NaN 42 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00000000 NaN NaN 0 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00000000 NaN NaN 42 0 0 0 0 0 0 0 0 0 +ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites +ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00 NaN NaN 42 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00 NaN NaN 0 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00 NaN NaN 42 0 0 0 0 0 0 0 0 0 +##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table +VariantSummary CompRod EvalRod JexlExpression Novelty nSamples nProcessedLoci nSNPs TiTvRatio SNPNoveltyRate nSNPsPerSample TiTvRatioPerSample SNPDPPerSample nIndels IndelNoveltyRate nIndelsPerSample IndelDPPerSample nSVs SVNoveltyRate nSVsPerSample +VariantSummary dbsnp input_0 none all 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none known 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none novel 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 + diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf --- a/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf +++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -10,7 +10,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -27,5 +27,6 @@ ##contig=<ID=phiX174,length=5386> ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta +##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . AC=0;AF=0.00;AN=0;DP=0;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . AC=0;AF=0.00;AN=0;DB;DP=0;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -25,13 +25,13 @@ #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations": --useAllAnnotations #else: - #if str( $annotations_type.annotations ) != "None": + #if $annotations_type.annotations: #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ): --annotation "${annotation}" #end for #end if #end if - #if str( $exclude_annotations ) != "None": + #if $exclude_annotations: #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ): --excludeAnnotation "${annotation}" #end for @@ -383,6 +383,7 @@ <param name="input_variant_bti" /><param name="annotations_type_selector" value="choose" /><param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" /> + <param name="additional_annotations" value="0" /><param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /><param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /> diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -12,7 +12,7 @@ -T "ValidateVariants" -et "NO_ET" ##ET no phone home - --num_threads 4 ##hard coded, for now + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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