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Created with Raphaël 2.2.03Jun229May130Apr2923222120181716158763131Mar3014Jan13109820Dec1912Nov25Oct2217Sep29Aug2829Jul1721Jun12331May292827232215141086130Apr2928Mar2726211219Feb21Jan1017Sep141231Jul28Jun271311May16Apr11530Mar282722128762128Feb27261519Jan30Nov292827242387Rename 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 statusRevert "use clone git strategy"Show sacct -j output on status parsing failureuse clone git strategyUse consistent flags for sbatchUpdate slurm-cluster-statusPut shebang in custom script.Merge branch 'BQSR' into no-mergeCall GATK baserecalibrate on readgroup bam filesUse pwd for current folder in PATHDrop the bash PATH cache