cluster.riboraptor.slurm.yaml

__default__:
    q: 'cmb'
    time: '12:00:00'
    pmem: '4000MB'
    mem: '4000MB'
    vmem: '61000MB'
    cores: 1
    logdir: '/home/cmb-06/as/skchoudh/logs/'
    out: '/home/cmb-06/as/skchoudh/logs/{rule}.{wildcards}.out'
    err: '/home/cmb-06/as/skchoudh/logs/{rule}.{wildcards}.err'

create_index:
    cores: 16
    mem: '4000MB'

create_rsem_index:
    cores: 16
    mem: '4000MB'

rsem_tx_level_counts:
    cores: 16
    mem: '4000MB'

map_star:
    time: '12:00:00'
    cores: 16
    mem: '4000MB'

count_exon:
    time: '24:00:00'
    mem: '4000MB'

count_cds:
    time: '24:00:00'
    mem: '4000MB'

create_uniq_bedgraph_from_bam:
    time: '12:00:00'
    cores: 16
    mem: '40gb'

count_exon:
    time: '24:00:00'
    mem: '60000MB'

create_uniq_bedgraph_from_bam:
    time: '12:00:00'
    cores: 16
    mem: '40gb'

create_uniq_bigwig_from_uniq_bedgraph:
    time: '12:00:00'
    cores: 1
    mem: '10gb'

create_uniqmulti_bigwig_from_uniqmulti_bedgraph:
    time: '12:00:00'
    cores: 1
    mem: '10gb'

fragment_length_pickle:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

infer_experiment:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

merge_bams:
    time: '12:00:00'
    cores: 16
    mem: '40gb'

merge_tx_bams:
    time: '12:00:00'
    cores: 16
    mem: '40gb'

metagene_coverage_CDS:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

metagene_coverage_UTR3:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

metagene_coverage_utr5:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

pickle_counts_cds:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

pickle_counts_utr3:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

pickle_counts_utr5:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

plot_fragment_length_distributon:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

plot_metagene_plot_normalized_CDS:
    time: '12:00:00'
    cores: 1
    mem: '40gb'

sort_by_name:
    time: '12:00:00'
    cores: 16
    mem: '40gb'

counts_to_tpm:
    time: '12:00:00'
    mem: '10gb'

pickle_tRNA_counts:
    time: '12:00:00'
    mem: '10gb'

extract_uniq_mapping:
    time: '12:00:00'
    mem: '10gb'
    cores: 16