This is a modular Snakemake workflow for processing long-read sequencing data (pacbio HiFi or ONT) to generate haplotype assigned methylation and to perform differential methylation analysis. To run this pipeline, it requires phased genome assemblies (hap1 and hap2; doesn't have to be trio phased) and modbam files including methylation with MM and ML tags.
try to run the pipeline something like:
mkdir -p log; snakemake --ri --jobname "{rulename}.{jobid}" \
--drmaa " -l centos=7 -V -cwd -j y -o ./log -e ./log -l h_rt={resources.hrs}:00:00 \
-l mfree={resources.mem}G -pe serial {threads} -w n -S /bin/bash" -w 60 \
-k -j 180 -p --resources load=100 --resources pbcpg=300 --reason