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slurm_config.json
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{
"__default__" : {
"name" : "AllMine {rule} [{wildcards}]",
"partition" : "lm.q",
"time" : "72:00:00",
"ntasks" : 1,
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 2000,
"errorStrategy" : "retry",
"maxRetries" : 2,
"cache" : "deep",
"maxErrors" : 10
},
"fastp_paired" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 7000
},
"fastp_single" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 4000
},
"fastqc_paired" : {
"mem-per-cpu-mb" : 6000
},
"fastqc_single" : {
"mem-per-cpu-mb" : 3000
},
"multiQC" : {
"mem-per-cpu-mb" : 1000,
"job-name" : "AllMine.{rule}",
"output" : "~/logs/{rule}.out",
"error" : "~/logs/{rule}.err"
},
"STAR_index" : {
"mem-per-cpu-mb" : 200000,
"cpus-per-task" : 20,
"job-name" : "AllMine.{rule}",
"output" : "~/logs/{rule}.out",
"error" : "~/logs/{rule}.err"
},
"STAR_REindex" : {
"mem-per-cpu-mb" : 200000,
"cpus-per-task" : 20,
"job-name" : "AllMine.{rule}",
"output" : "~/logs/{rule}.out",
"error" : "~/logs/{rule}.err"
},
"bwa_index" : {
"mem-per-cpu-mb" : 10000,
"cpus-per-task" : 10,
"job-name" : "AllMine.{rule}",
"output" : "~/logs/{rule}.out",
"error" : "~/logs/{rule}.err"
},
"star_pe_FP" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 10000
},
"star_pe_SP" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 10000
},
"star_se_FP" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 10000
},
"star_se_SP" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 10000
},
"bwa_paired" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 20000
},
"bwa_single" : {
"cpus-per-task" : 10,
"mem-per-cpu-mb" : 20000
},
"varscan" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 5000
},
"snpEff" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 3000
},
"snpSift" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 1000
},
"make_report" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 1000
},
"whatshap" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 1000
},
"bam_index" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 2000
},
"annovar" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 6000
},
"vcf4_to_avinput" : {
"cpus-per-task" : 1,
"mem-per-cpu-mb" : 4000
}
}