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EXAMPLE_cluster_singularity_slurm_remap_preprocessing.json
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EXAMPLE_cluster_singularity_slurm_remap_preprocessing.json
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{
"__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.replicat_name}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.replicat_name}_slurm.err",
"mail-type":"BEGIN,END",
"mail-user":"first.last@mail.com"
},
"aria2":
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "2:00:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.fastq_name}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.fastq_name}_slurm.err"
},
"trim_galore" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "9:00:00"
},
"bowtie2" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "16",
"ntasks" : "1",
"time" : "7:00:00"
},
"delete_trim_paired" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "0:05:00",
"stdout" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.out",
"stderr" : "/absolute/path/to/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.err"
},
"remove_mismatch" :
{
"job-name" : "RMmismatch",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"time" : "8:00:00"
},
"samtools_sort" :
{
"job-name" : "sort",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"time" : "4:20:00"
},
"samtools_remove_pcr_duplicate" :
{
"job-name" : "RMpcrdup",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "10:00:00"
},
"macs2" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "15G",
"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"
},
"samtools_remove_unmapped" :
{
"job-name" : "RMunmapped",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "5:30:00"
},
"sam_to_bam":
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"memory" : "10G",
"time" : "18:00:00"
}
}