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Created with Raphaël 2.2.028Apr252120191431Mar1710323Feb1716106131Jan2726252423161325Nov151410987428Oct262524211411723Sep1226Aug25232219181185229Jul2826184130Jun2322171630May8Apr18Mar987432125Feb2415141110928Jan27261918171411416Dec1514626Nov1715131211109829Oct28130Sep241723Aug20181029Jul2721201998752130Jun2928252221161514111072131May2825211920Apr1514131230Mar29252322191817118424Feb22211918169428Jan21158628Dec24221615119130Nov272625191712111096543230Oct2827262216151312987652129Sep24232116151411109Set stable versionupdate svprep docker imageadjust AnnotateInsertedSequence inputsfix lint issueupdate peach, add rose, etc.update linx and lilacupdate samtools viewupdate various hmftools, add task for svprep gridssmake reference optional in amber and cobaltMerge branch 'shallow_mode' into 5.31_updateMerge branch 'develop' into 5.31_updateMerge pull request #318 from biowdl/shallow_modev5.1.0v5.1.0update parameter_meta and changelogshallow_modeshallow_modeadd purple options needed for shallow modeadd option to enable/disable ploy-g trimming to fastp taskfastp_updatefastp_updateMerge pull request #317 from biowdl/fastp_updateadd some options to disable filters in fastpMerge pull request #316 from biowdl/fastpadd some missing options to hmftools sage and cobaltMerge branch 'fastp' into 5.31_updateMerge remote-tracking branch 'origin/develop' into 5.31_updateMerge remote-tracking branch 'origin/develop' into fastpMerge pull request #312 from biowdl/somaticSvupdate scriptssomaticSvsomaticSvupdate changelogMerge remote-tracking branch 'origin/develop' into somaticSvupdate scriptsfastpfastpupdate changelogMerge remote-tracking branch 'origin/develop' into fastpMerge pull request #315 from biowdl/BIOWDL-604Add missing interpunctionUpdate changelog with separatorCharAllow a custom separator charadd samples option to bcftools viewfix gridss somatic filter output paths?fix output paths gridss somatic filteradd missing fasta index input to gridss GeneratePonBedpegive delly more time, specify normal ordinal in gridss GeneratePonBedpe commandupdate parameter_metaadd index to delly call inputs as well