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Created with Raphaël 2.2.024Jun2322173229May130Apr2923222120181716158763131Mar3014Jan13109820Dec1912Nov25Oct2217Sep29Aug2829Jul1721Jun12331May292827232215141086130Apr2928Mar2726211219Feb21Jan1017Sep141231Jul28Jun271311May16Apr11530Mar282722128762128Feb27261519Jan30Nov292827242387Add snakemake logic for coverage bed filesSnakemake 5.19.3 has 'insert' as a reserved wordAdd picard DuplicationMetrics to stats.jsonSimplify the structure of the coverage dataAdd test for mode insert sizeAdd picard AlignmentSummaryMetricsSwitch to contains_regex for vcf contentPrettify the pytest-workflow yaml filesFix table formatting in ReadmeAdd test for stats.json with multiple samplesRename bedfile to targetsfileClean up collect stats no file passingIntegrate the picard HsMetrics into the stats.json fileAdd picard CollectHsMetrics to the pipelineAdd a singularity prefix to the snakemake profileAdd picard insertSize metrics tot stats.jsonConsolidate collectstats into a single ruleRemove newlinesSwitch to lambda expression instead of external functionMake formatting more consistentSwitch to using rule-based dependenciesRename final bamfile to {sample}.bamAdd picard multiple metricsEnable json output for multiqcUpdate pytest-workflow requirementMerge branch 'devel' of https://git.lumc.nl/klinische-genetica/capture-lumc/hutspot into develAdd test for raw bases and readsIncrease memory for covstatsIncrease scatterregion memory limitAdd memory requirement to scatterregionsMake sure relative paths are handled properlyRename libraries in config to read_groupsClean up coverage stats header namesSwitch to using a --configfileMerge branch 'no-merge' into 'devel'use plain pytestupdate singularity imageAdd workflow-threads to speed up the testsRemove debugging and enable all tests for gitlab-citry multiple attempts to get status