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Created with Raphaël 2.2.028Jan272423222120171615141310987617Dec12111096227Nov262519765131Oct3028159872127Sep26252423201817161312111096543229Aug2216151413126542131Jul2928272619181716151211109832127Jun26252421201918171413121165429May2723222120151397629Apr262524231817161585429Mar2521201918141312875126Feb2522212019add index for commonvariantsitesUpdate CHANGELOG.Fix issue where Centrifuge could not locate index files.Merge branch 'develop' of https://github.com/biowdl/tasks into developfix bug where text to file does not work with other shells than bashMerge pull request #176 from biowdl/BIOWDL-385Merge branch 'develop' into BIOWDL-385Merge pull request #175 from biowdl/BIOWDL-319Merge branch 'develop' into BIOWDL-319Merge pull request #177 from biowdl/BIOWDL-386Update CHANGELOG.BIOWDL-386BIOWDL-386Fix issue where centrifuge would fail on incorrect paths.Merge branch 'develop' into BIOWDL-319BIOWDL-319BIOWDL-319Merge pull request #171 from biowdl/CNV_callingupdate changelogBIOWDL-385BIOWDL-385increase default memory for BWA memupdate changelogmake memory configurable in fastqcMerge remote-tracking branch 'origin/develop' into CNV_callingupdate changelogMerge pull request #173 from biowdl/BIOWDL-387Merge branch 'develop' into BIOWDL-387Merge pull request #174 from biowdl/BIOWDL-386fix various issuesCNV_callingCNV_callingtypoUpdate CHANGELOG.Centrifuge should use -U instead of -1 with single end data.update parameter metaBIOWDL-387BIOWDL-387use broad's gatk containerupdate changelogfix mkdir in CreateReadCountPanelOfNormalsadd text to file tasktypotyposupdate changelogfix typoadd intersect bed taskfix missing backslashupdate changelogset pipefail to prevent errors in bed files