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Created with Raphaël 2.2.015Oct1312987652129Sep24232116151411109742126Aug2420191817141312111076529Jul2827232221201716151397632130Jun29262524232219181716151211109854228May20191815141311876130Apr282120151410987632131Mar3026252423201918161312119325Feb24201312111076543Merge pull request #252 from biowdl/bugfixRemove most inputsremove redundant G in -Xmx in snpeffMerge branch 'develop' into bugfixbugfixbugfixMerge branch 'develop' into Pacbio-variantcallingMerge pull request #257 from biowdl/bcftools_add_tmpadd tmpDir to parameter_meta sectionadd tmpDir input to specify temporary directory when sorting.Update CHANGELOG.mdMerge pull request #256 from biowdl/optional-indexingMerge branch 'develop' into optional-indexingoptional-indexingoptional-indexingupdate CHANGELOGremove outputType and indexing instead based on extension of the fileAdd parameter meta for CollectHsMetricsUpdate parameter metaUpdate picard.wdlUpdate CHANGELOG.mdUpdate CHANGELOG.mdUpdate CHANGELOG.mdUpdate CHANGELOG.mdMerge pull request #253 from biowdl/BIOWDL-499Update changelogAdd whatshap tasksAdd deepvariant tasksAdd HsMetrics and VariantcallingMetrics to picardIncrease runtime and add sample name for pbmm2Make intervals optional for gatk GenotypeGVCFsAdd task for indexing PacBio bam filesSimplify lima output structureAdd bam index file as required input for isoseqEnsure that the index and bamfiles are in the same folderUpdate parameter_meta.fix bcftools filterUpdate samtools.wdlUpdate CHANGELOG.mdfix whitespaceMake sure the bam and pbi files are in the same foldersimplify-limasimplify-limaSimplify the lima task output structurefix bcftools filterUpdate Changelog