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EXAMPLE_cluster_singularity_slurm_bigwig.json
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EXAMPLE_cluster_singularity_slurm_bigwig.json
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{
"__default__":
{
"project-name":"b097",
"job-name" : "{rule}",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "2:30:00",
"memory" : "5G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.replicat_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.replicat_name}_slurm.err",
"mail-type":"BEGIN,END",
"mail-user":"hammal_10@hotmail.fr"
},
"aria2":
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "12:00:00",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.fastq_name}_slurm.out",
"stderr" : "/scratch/fhammal/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" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.replicat_name_paired}_slurm.err"
},
"samtools_remove_unmapped" :
{
"job-name" : "RMunmapped",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "5:30:00"
},
"remove_mismatch" :
{
"job-name" : "RMmismatch",
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"time" : "5:00:00"
},
"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" : "5:00:00"
},
"macs2_bigwig" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"removing_weird_chromosome" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"sort_bedgraph" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"clipping_bedgraph" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"memory" : "11G",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"bedgraph_to_bigwig" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"time" : "18:00:00",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}.{wildcards.experiment_name}_slurm.err"
},
"merge_bam" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_FRiP" :
{
"queue" : "remap",
"node" : "1",
"thread" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_NSC_RSC" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "2",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
},
"quality_all" :
{
"partition" : "skylake",
"node" : "1",
"thread" : "1",
"ntasks" : "1",
"stdout" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.out",
"stderr" : "/scratch/fhammal/remap-pipeline/4.preprocessing/log/{rule}_{wildcards.experiment_name}_qsub.err"
}
}