Makefile

#The list of subcommands
help:
	@echo "Avaiable subcommands"
	@echo "\t- run"
	@echo "\t- clean"

run:
	@bash -c "module unload snakemake; \
	module load snakemake/7.25.0 ; \
	snakemake --cluster 'sbatch -c {params.cpu} --mem {params.mem} --partition=fast --account=2427_data_master' -c 3000 -j  500  --rerun-incomplete --rerun-trigger mtime"

dry:
	@bash -c "module unload snakemake; \
	module load snakemake/7.25.0 ; \
	snakemake --cluster 'sbatch -c {params.cpu} --mem {params.mem} --partition=fast --account=2427_data_master' -c 3000 -j  500  --rerun-incomplete --rerun-trigger mtime -n -p"

#Clean unnecessary files 
clean: 
	@rm -f slurm*.out
	

graph:
	@bash -c "module unload snakemake; \
	module load snakemake/7.25.0 ; \
	module load graphviz/2.40.1 ; \
	snakemake --dag | dot -Tpng > graph.png"

rulegraph:
	@bash -c "module unload snakemake; \
	module load snakemake/7.25.0 ; \
	module load graphviz/2.40.1 ; \
	snakemake --rulegraph | dot -Tpng > rulegraph.png"

queue:
	@squeue -u $$USER