How to communicate cluster resources to rules.

# SOLUTION 1

rule delly:
    input:
        bamlist="{batch}/bamlist.list",
        excluded="exclusion/excluded.bed",
        reference = REFERENCE,
        fai = REFERENCE + ".fai"
    output:
        "{batch}/delly/delly_{chrom}_{svtype}.bcf"
    params:
        template = EMPTY_TEMPLATE,
        reference = os.path.abspath(REFERENCE)
    threads:
        get_threads("delly", 4)
    log:
        stdout = "{batch}/logs/delly/{chrom}_{svtype}.o",
        stderr = "{batch}/logs/delly/{chrom}_{svtype}.e"
    shell:
        "export  OMP_NUM_THREADS={threads} ; "
        "delly.py -b {input.bamlist} -c {wildcards.chrom}"
        " -g {params.reference} -x {input.excluded} -t {wildcards.svtype}"
        " -o {output} -e {params.template}"
        " 1>{log.stdout} 2>{log.stderr}"


with 

def get_threads(rule, default):
    cluster_config = snakemake.workflow.cluster_config
    if rule in cluster_config and "threads" in cluster_config[rule]:
        return cluster_config[rule]["threads"]
    if "default" in cluster_config and "threads" in cluster_config["default"]:
        return cluster_config["default"]["threads"]
    return default



## SOLUTION 2 
#config.yaml
resources: resources.yaml

# Snakefile
with open(config["resources"]) as yml:
    config.update(yaml.load(yml))

rule rsem_count:
    input:
        expand("Results/Rsem_Index/" + os.path.splitext(os.path.basename(config["fasta_ref"]))[0]+".{suffix}", suffix=RSEM_SUFFIX[1:]),
        rsem_idx="Results/Rsem_Index/" + os.path.splitext(os.path.basename(config["fasta_ref"]))[0]+".grp",
        bam=get_RSEM_inbam
    output:
        "Results/{dir}/{prefix}.genes.results",
        "Results/{dir}/{prefix}.isoforms.results"
    params:
        forward_prob = lambda wildcards : table[table.forward_read.str.contains('^' + wildcards.prefix)]["oriented"].tolist()[0],
        mode = lambda wildcards : "--paired-end" if table[table.forward_read.str.contains('^' + wildcards.prefix)]["reverse_read"].any() else "" ,
        prefixOut="Results/{dir}/{prefix}"
    threads: config["rsem_count"]["cpu"]
    shell:
        "rsem-calculate-expression --ci-memory 30000 {params.mode} --bam --no-bam-output --estimate-rspd --calc-ci --seed 12345 -p {threads} --forward-prob {params.forward_prob} {input.bam} `echo {input.rsem_idx} | sed 's/.grp//'` {params.prefixOut}"

# launch Snakemake
snakemake \
    --snakefile $SNAKEDIR/Snakefile \
    --configfile config.yaml \
    --jobs 999 --cluster-config resources.yaml --cluster "sbatch -p unlimitq -e LOG/run1/%x.err -o LOG/run1/%x.out --cpus-per-task={cluster.cpu} --time={cluster.time} --mem-per-cpu={cluster.mem}" \
    --printshellcmds --latency-wait 30 --until star_aln_pass1 --notemp