HOWTO

#rulegraph
snakemake --rulegraph | dot -Tsvg > rulegraph.svg

#cancel jobs from x to y
for f {123123..4234829}; do scancel $f; done
#or simply
scancel {9417393..9417408}

#cancel all pending jobs
scancel -t PENDING -u leeming

#sumbit -c specifies the clusterconfig. Resources for each job will be taken from "default" unless specified in the job 
./MitoComp -t slurm -c data/cluster-config-VSC4-SLURM.yaml.template 

#dry run. Specify runmode via "./MitoComp -m assembly" or "./MitoComp -m all" (or nothing) will run the complete pipeline
./MitoComp -t slurm -c data/cluster-config-VSC4-SLURM.yaml.template --dry
 
#use -t serial to run locally - good to test single rule
./MitoComp -t serial -c data/cluster-config-VSC4-SLURM.yaml.template -s "--until align -j1"  

#free up space in .singularty directory (always in home so limited space)
singularity cache clean

#add bind point. can access data in sub-directories of another user - avoids copying raw data. N.B. requires permissions
./MitoComp -t slurm -c data/cluster-config-VSC4-SLURM.yaml.template -i "-B /gpfs/data/fs71312/hahnc/RAW/Monogeniac_Illumina/"