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Created with Raphaël 2.2.029Apr23222120181716158763131Mar3014Jan13109820Dec1912Nov25Oct2217Sep29Aug2829Jul1721Jun12331May292827232215141086130Apr2928Mar2726211219Feb21Jan1017Sep141231Jul28Jun271311May16Apr11530Mar282722128762128Feb27261519Jan30Nov292827242387Switch 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 cacheInject slurm submission into integration testUse environment conda to run integrationTry using pip for slurm runnerRemove docker image from slurm runnerAdd singularity anchorset BASETEMP and remove functional tagUpdate gitlab-ci testsRemove unneeded scripts, rules and containersRemove code to calculate vcf statsFix tests, remove vcf statistics from stats fileIntegrate cutadapt summary in stats.tsvAdd detailed metrics output to testAdd tests for two samplesAdd metrics to default outputAdd collect metrics scriptUpdate multiqc, add logfile to cutadaptAdd summary output for cutadaptNo longer merge fastq filesCreate bamfile, fastq statistics disabledReorganise the test data, add readgroups testUpdate graphUpdate readme and example configuration filesMerge branch 'gvcf-bin' into devel