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Created with Raphaël 2.2.028Jul242226Jun25242322173229May130Apr2923222120181716158763131Mar3014Jan13109820Dec1912Nov25Oct2217Sep29Aug2829Jul1721Jun12331May292827232215141086130Apr2928Mar2726211219Feb21Jan1017Sep141231Jul28Jun271311May16Apr11530Mar282722128762128Feb27261519Jan30Nov292827242387Add memory settings for hs_metrics and multiple_metricsMake sure female-threshold is a floatMerge branch 'devel' of git.lumc.nl:klinische-genetica/capture-lumc/hutspot into develAdd slurm cluster configurationIncrease memory for bed_to_intervalMerge branch 'revert-1b7d807f' into 'devel'Revert "Remove explicit tmp folder"Increase memory for bed_to_intervalRemove explicit tmp folderMerge branch 'bed-coverage' into develUpdate to temporary version of gvcf2coverageUpdate mulled containerAdd new container for gvcf2coverageMerge branch 'bed-coverage' into 'devel'Update slurm cluster statusUpdate tags for testsFix dry run tests for coverage bedAdd optional coverage bedfilesAdd 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}.bam