snakemake \
  -s Snakefile \
  -j 30 \
  --latency-wait 120 \
  --use-conda \
  -n

conda activate viz_snakemake
snakemake -s Snakefile --dag | dot -Tpng > ruledag.png

snakemake \
  -s Snakefile \
  -j 60 \
  --latency-wait 120 \
  --use-conda \
  --cluster "sbatch -A seyedam_lab --partition=highmem --mem={resources.mem_gb}GB -c {resources.threads} --mail-user=freese@uci.edu --mail-type=START,END,FAIL --time=72:00:00" -n

Requirements:

CLI * samtools * minimap2 * faidx Python * PyRanges * TranscriptClean * TALON * LAPA * Cerberus * Swan * pydeseq2