Updated citation for snakePipes Fixed replicate check for samples with trailing spaces in names Fixed input filtering in CSAW Several allele-specific RNAseq fixes ATACseq peakQC is now run on fragment-size filtered bam Fixed Salmon output (Number of Reads output in "*counts.tsv" files and file naming) Fixed CSAW QC plot error with single end reads Updated histone HMM environment to a working conda version Salmon_wasabi is now a localrule