config.json

{
  "run_processes": {
    "genome_indexing": false,
    "fastq_trimming": false,
    "alignment": false,
    "BAM_sorting": false,
    "remove_duplicates": false,
    "BAM_filtering": false,
    "BAM_indexing": false,
    "BAM_stats": false,
    "gene_counts": false,
    "splicing_analysis": false,
    "summarize_results": false
  },
  "data_paths": {
    "input_list": "",
    "index_dir": "",
    "fasta_file": "",
    "annotation_file": "",
    "trimmed_fastq_dir": "",
    "out_bam_dir": "",
    "gene_counts_dir": "",
    "contrasts_file": "",
    "splicing_dir": "",
    "report_dir": ""
  },
  "processes": {
    "genome_indexing": {
      "max_RAM": "180000000000",
      "queue": "",
      "time": "2h",
      "memory": "180GB",
      "num_threads": 5
    },
    "fastq_trimming": {
      "quality_thres": 20,
      "min_length": 35,
      "queue": "",
      "time": "2h",
      "memory": "32GB",
      "multithreaded": true
    },
    "alignment": {
      "queue": "",
      "time": "2h",
      "memory": "180GB",
      "num_threads": 5
    },
    "BAM_sorting": {
      "queue": "",
      "time": "2h",
      "memory": "16GB",
      "num_threads": 5
    },
    "remove_duplicates": {
      "remove_seq_duplicates": true,
      "queue": "",
      "time": "2h",
      "memory": "40GB"
    },
    "BAM_filtering": {
      "quality_thres": 30,
      "queue": "",
      "time": "1h",
      "memory": "2GB",
      "num_threads": 5
    },
    "BAM_indexing": {
      "queue": "",
      "time": "1h",
      "memory": "2GB",
      "num_threads": 5
    },
    "BAM_stats": {
      "queue": "",
      "time": "1h",
      "memory": "2GB",
      "num_threads": 5
    },
    "gene_counts": {
      "algo": "HTSeq",
      "strandedness": 2,
      "queue": "",
      "time": "6h",
      "memory": "32GB",
      "num_threads": 5
    },
    "splicing_analysis": {
      "strandedness": 2,
      "read_length": 100,
      "cutoff_diff": 0.0001,
      "use_paired_stats": false,
      "detect_novel_splice": false,
      "min_intron_len": 50,
      "max_exon_len": 500,
      "queue": "",
      "time": "2h",
      "memory": "14GB",
      "num_threads": 5
    },
    "summarize_results": {
      "queue": "",
      "time": "1h",
      "memory": "2GB"
    }
  },
  "container_dir": "",
  "nf_work_dir": "",
  "run_locally": false,
  "save_all_BAM": false
}