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Created with Raphaël 2.2.022Apr2120181716158763131Mar3014Jan13109820Dec1912Nov25Oct2217Sep29Aug2829Jul1721Jun12331May292827232215141086130Apr2928Mar2726211219Feb21Jan1017Sep141231Jul28Jun271311May16Apr11530Mar282722128762128Feb27261519Jan30Nov292827242387Drop 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 develAdd tests for multiple known site vcf filesAdd tests for bedfileMove refflat results to the coverage folderAdd tests for refFlat fileRemove global python variablesAdd the vcf index (tbi) to the pipeline outputMark the scattered vcf outputs as temporaryAdd constant GVCF bands with 20GQ incrementsAdd a parameter for SCATTER_SIZEAdd g.vcf file to default output of the pipelineIncrease scatter size to 1 billionMerge scattered vcf files with checkpointAdd different chunk to expected outputAdd input constraintSwitch to using snakemake checkpointsWIP: move to single sample calling