Releases · huishenlab/Biscuit_Snakemake_Workflow

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

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