{
  "__default__" :
  {
    "queue": "6hours",
    "time": "01:00:00",
    "threads": "1",
    "mem": "4G",
    "name": "{rule}.{wildcards}",
    "out": "logs/cluster/{rule}.{wildcards}-%j-%N.out"
  },
  "create_index_star":
  {
    "time": "06:00:00",
    "threads":"12",
    "mem":"45G"
  },
  "extract_transcripts_as_bed12":
  {
    "time": "00:30:00",
    "threads":"1",
    "mem":"1G"
  },
  "extract_transcriptome":
  {
    "time": "00:30:00",
    "threads":"1",
    "mem":"1G"
  },
  "create_index_salmon":
  {
    "time": "03:00:00",
    "threads":"8",
    "mem":"10G"
  },
  "create_index_kallisto":
  {
    "time": "00:30:00",
    "threads":"1",
    "mem":"10G"
  },
  "index_genomic_alignment_samtools":
  {
    "time": "00:30:00",
    "threads":"1",
    "mem":"500M"
  },
  "star_rpm":
  {
    "time": "00:30:00",
    "threads":"4",
    "mem":"15G"
  },
  "rename_star_rpm_for_alfa":
  {
    "time": "03:00:00",
    "threads":"1",
    "mem":"32G"
  },
  "calculate_TIN_scores":
  {
    "time": "06:00:00",
    "threads":"8",
    "mem":"15G"
  },
  "merge_TIN_scores":
  {
    "time": "00:05:00",
    "threads":"1",
    "mem":"500M"
  },
  "plot_TIN_scores":
  {
    "time": "00:05:00",
    "threads":"1",
    "mem":"500M"
  },
  "salmon_quantmerge_genes":
  {
    "time": "00:05:00",
    "threads":"1",
    "mem":"500M"
  },
  "salmon_quantmerge_transcripts":
  {
    "time": "00:05:00",
    "threads":"1",
    "mem":"500M"
  },
  "generate_alfa_index":
  {
    "time": "02:00:00",
    "threads":"4",
    "mem":"1G"
  },
  "alfa_qc":
  {
    "time": "00:30:00",
    "threads":"1",
    "mem":"500M"
  },
  "alfa_qc_all_samples":
  {
    "time": "01:00:00",
    "threads":"1",
    "mem":"500M"
  },
  "pe_fastqc":
  {
    "time": "01:00:00",
    "threads":"2",
    "mem":"1G"
  },
  "fastqc":
  {
    "time": "01:00:00",
    "threads":"2",
    "mem":"1G"
  },
  "pe_remove_adapters_cutadapt":
  {
    "time": "06:00:00",
    "threads":"8",
    "mem":"1G"
  },
  "remove_adapters_cutadapt":
  {
    "time": "06:00:00",
    "threads":"8",
    "mem":"1G"
  },
  "pe_remove_polya_cutadapt":
  {
    "time": "06:00:00",
    "threads":"8",
    "mem":"1G"
  },
  "remove_polya_cutadapt":
  {
    "time": "06:00:00",
    "threads":"8",
    "mem":"1G"
  },
  "pe_map_genome_star":
  {
    "time": "06:00:00",
    "threads":"12",
    "mem":"50G"
  }, 
  "map_genome_star":
  {
    "time": "06:00:00",
    "threads":"12",
    "mem":"50G"
  }, 
  "pe_quantification_salmon":
  {
    "time": "03:00:00",
    "threads":"6",
    "mem":"10G"
  }, 
  "quantification_salmon":
  {
    "time": "03:00:00",
    "threads":"6",
    "mem":"10G"
  }, 
  "pe_genome_quantification_kallisto":
  {
    "time": "03:00:00",
    "threads":"8",
    "mem":"15G"
  },
  "genome_quantification_kallisto":
  {
    "time": "03:00:00",
    "threads":"8",
    "mem":"15G"
  }
}