EXAMPLE_cluster_singularity_slurm_Remap_postprocessing.json

{
"__default__":
{
"project-name":"project_name",
"job-name" : "{rule}",
"partition" : "queue_name",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "2:30:00",
"memory" : "5G",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_slurm.err",
"mail-type":"BEGIN,END",
"mail-user":"first.last@mail.com"
},

"merge_bam" :
{
"partition" : "skylake"
},

"quality_FRiP" :
{
"partition" : "skylake"
},

"quality_NSC_RSC" :
{
"partition" : "skylake",
"thread" : "2",
"memory" : "15G"
},

"quality_all" :
{
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.err"
},

"quality_all_experiments" :
{
"partition" : "skylake"
},

"filtering_quality_all" :
{
"time" : "03:00:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.err"
},

"graph_quality_all" :
{
"time" : "03:00:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.err"
},

"creating_remap_catalogue_bed" :
{
"time" : "03:00:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.err"
},

"sort_remap_bed" :
{
"time" : "06:00:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_slurm.err"
}

}