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Created with Raphaël 2.2.020Jan19181514121110987654330Dec292827171475230Nov20191413121110931Oct20Sep14131211109131Aug27262524201916151413121110876543Merge branch 'develop' into 'master'Update errors in readmeMerge branch '108-samtools.mem' into 'develop'Update DAGUse 1 less process for samtools threading and limit memto 75% of availableMake sampled align use > 32GB nodes on BioHPCCatch error if fastq file error grepFix fastqc error detectionAdd back ends manual to parse ci unitAdd back ends manual to ci unit for parse, but manualAdd unexpected meta and fastq structure error ci integration testsAdd excape to bracket in echoRemove ends manual from parse metadata unit ciAdd premature fail execution run upload with fastq file errorFix no fastq error detailFix no fastq's present in inputBagUpgrade version to v1.0.3Fix file structure error detectionFix if thenFix endsManual assignmentFix fastq file error detectionMake dummy fastqc output if failDetect malformed fastqsFix spike/species asignment for unexpectedFix python else syntacFurther remove parsing restrictions from stranded/spike/speciesRemove ability to count fastqs manually from file.csvDon't parse manual ends from file.csv anymoreFix elifHandle blank endness betterRemove redundant check for multiple fastqs in parse metadataAllow .R[1,2] and _R[1,2] fastqsFilter input bag export config to only get fastq's matching conventionOnly used fastq's named correctlyPhysically move fastqc process upFix fastq run before trimMove fastqc before trimUpdate changelogAllow unexpected values for stranded/spike/speciesUpdate changelog