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Created with Raphaël 2.2.022May1612542128Apr252120191431Mar1710323Feb1716106131Jan2726252423161325Nov151410987428Oct262524211411723Sep1226Aug25232219181185229Jul2826184130Jun2322171630May8Apr18Mar987432125Feb2415141110928Jan27261918171411416Dec1514626Nov1715131211109829Oct28130Sep241723Aug20181029Jul2721201998752130Jun2928252221161514111072131May2825211920Apr1514131230Mar29252322191817118424Feb22211918169428Jan21158628Dec24221615119130Nov272625191712111096543230Oct2827262216151312987652129Sep242321161514add output for hmftools rose5.31_update5.31_updatefix issue with java permissions in orangeuse digest instead of tag for cuppa dockertypocleanupfix linx outputstypoupdate inputs for annotateinsertedsequencesgive SvPrepDepthAnnotator more timetry using digest instead of tagtyposetting next versiondevelopdevelopStable version in changelogv5.2.0 masterv5.2.0 masterMerge pull request #320 from biowdl/BIOWDL-605Update classpathBIOWDL-605BIOWDL-605Update cutadapt and FastQCsetting next versionSet 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/somaticSv