Version 0.4.0

Note, this version is not compatible with previous versions of the pipeline

General Changes:

• Remove profile/ directory and adjust SLURM submit script accordingly
• Execute file permissions removed from .smk files
• Remove wildcard entry from SLURM log file name
• Update DAGs for single and five sample examples for both default and full pipelines
• Update README for pipeline

Configuration Changes:

• Versions of environmental modules updated
• Configuration variable names changed for consistent naming scheme
• Expand arguments to long name in args_list option of region_centered_bin_averages
• Group related items together
• Make items governing optional rules have the same style
• Move description of option closer to actual option
• Remove adaptase specific trimming option from default trimming options

Rule Changes:

• samtools flagstat moved out of biscuit_sifter rule into its own rule in qc.smk
• References to biscuit_blaster changed to biscuit_sifter
• Fix cyclic graph exception in region_centered_bin_averages rule
• Make rule for creating plot for percent of genome covered optional
• Fix bug where binned_averages wouldn't provide a helpful error message if input BED files were empty
• Allow user to pass additional flags to biscuit rules from configuration file
• Make use of parallelization in bgzip
• Make rules point to rule log files as best as possible
• Make use of parallelization for sorting in bitmap asset creation