cluster.json

{
    "fastp" :
    {
        "ncore" : 6,
        "memo" : 6000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.sample}",
        "logi" : "log_folder/fastp/{rule}_{wildcards.sample}.log"
    },
    "split_fastq" :
    {
        "ncore" : 6,
        "memo" : 3000,
        "jobtime" : "23:59",
        "jobname" : "{rule}_{wildcards.sample}",
        "logi" : "log_folder/split_fastq/{rule}_{wildcards.sample}.log"
    },
    "alignment" :
    {
        "ncore" : 12,
        "memo" : 3500,
        "jobtime" : "47:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}_{wildcards.flowcell}_{wildcards.lane}",
        "logi" : "log_folder/alignment/{rule}_{wildcards.reference}_{wildcards.sample}_{wildcards.flowcell}_{wildcards.lane}.log"
    },
    "sambamba_sort" :
    {
        "ncore" : 6,
        "memo" : 2500,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}_{wildcards.flowcell}_{wildcards.lane}",
        "logi" : "log_folder/sambamba_sort/{rule}_{wildcards.reference}_{wildcards.sample}_{wildcards.flowcell}_{wildcards.lane}.log"
    },
    "sambamba_merge" :
    {
        "ncore" : 6,
        "memo" : 3000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/sambamba_merge/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "sambamba_flagstat_1" :
    {
        "ncore" : 3,
        "memo" : 4000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/sambamba_flagstat_1/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "mark_duplicates" :
    {
        "ncore" : 6,
        "memo" : 7500,
        "jobtime" : "23:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/mark_duplicates/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "build_index" :
    {
        "ncore" : 6,
        "memo" : 2000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/build_index/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "sambamba_flagstat_2" :
    {
        "ncore" : 3,
        "memo" : 4000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/sambamba_flagstat_2/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "picard_metrics" :
    {
        "ncore" : 8,
        "memo" : 3000,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/{rule}/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "samtools_idxstats" :
    {
        "ncore" : 1,
        "memo" : 250,
        "jobtime" : "00:59",
        "jobname" : "{rule}_{wildcards.reference}_{wildcards.sample}",
        "logi" : "log_folder/{rule}/{rule}_{wildcards.reference}_{wildcards.sample}.log"
    },
    "sam_flags" :
    {
        "ncore" : 2,
        "memo" : 500,
        "jobtime" : "03:59",
        "jobname" : "{rule}_{wildcards.sample}_{wildcards.reference}_{wildcards.chrm}",
        "logi" : "log_folder/{rule}_{wildcards.sample}_{wildcards.reference}_{wildcards.chrm}.log"
    }
}