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Created with Raphaël 2.2.028Jan272423222120171615141310987617Dec12111096227Nov262519765131Oct3028159872127Sep26252423201817161312111096543229Aug2216151413126542131Jul2928272619181716151211109832127Jun26252421201918171413121165429May2723222120151397629Apr262524231817161585429Mar2521201918141312875126Feb2522212019Fix 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 filesadd various CNV calling tasksMerge pull request #172 from biowdl/BIOWDL-377