Quality-of-Life Improvements and Bugfixes

[koisland]

• Allow compressed/uncompressed fq, fastq, or bam files as input to nucfreq rules.
• Allow uncompressed fq or fastq files as input to concat_asm rules.
• Add better error message if missing reads for nucfreq rules.
• Add better error handling on empty in puts for bedminmax script.
• Improve contig start and stop parsing for make_new_cens_bed_file rule.
• Fix incorrect start-stop calculation in aggregating dna-brnn output.
• Add edge-case threshold for chrY in dna-brnn output filtering.
• Remove unused docker/ folder.