snakemake_config.yaml

# Resource allocation
guppy_threads: 20
guppy_mem_gb: 48
guppy_time_hr: 96
minimap2_threads: 10
minimap2_mem_gb: 48
minimap2_time_hr: 48
espresso_s_threads: 8
espresso_s_mem_gb: 96
espresso_s_time_hr: 60
espresso_c_threads: 8
espresso_c_mem_gb: 96
espresso_c_time_hr: 120
espresso_q_mem_gb: 96
espresso_q_time_hr: 120
visualize_mem_gb: 40
# Command options
use_annotated_junctions_with_minimap2: true
keep_espresso_c_temp: false
output_compatible_isoforms: true
# Visualization options
enable_visualization: false
visualization_path: './visualization/'
vis_normalize_counts: false
vis_target_gene: ''
vis_minimum_count: 1
vis_descriptive_name: 'ESPRESSO'
# Reference files
gtf_url: ''
gtf_name: 'gencode.v34lift37.annotation.gtf'
fasta_url: ''
fasta_name: 'ucsc.hg19.fasta'
# Input samples
# Template is shown here
samples:
  IMPACT_FC2_1:
    - guppy_config: 'dna_r9.4.1_450bps_fast.cfg'      
      fast5_dir: '~/20211207_BRCA_IMPACT_FC2_1/fast5/'
  IMPACT_FC2_2:
    - guppy_config: 'dna_r9.4.1_450bps_fast.cfg'      
      fast5_dir: '~/20211207_BRCA_IMPACT_FC2_2/fast5/'


# Executable paths
guppy_bin_path: '/path/to/guppy/ont-guppy-cpu_4.0.15/bin/'
conda_wrapper: './conda_wrapper'
espresso_path: './alpha1.2.2'