snakemake_config.yaml

# Resource allocation
guppy_gpu_name: 'a100'
guppy_gpus: 1
guppy_mem_gb: 48
guppy_threads: 20
guppy_time_hr: 48
combine_c_for_q_mem_gb: 8
combine_c_for_q_time_hr: 12
create_corrected_sams_mem_gb: 16
create_corrected_sams_threads: 10
create_corrected_sams_time_hr: 48
espresso_c_mem_gb: 32
espresso_c_threads: 4
espresso_c_time_hr: 12
espresso_q_mem_gb: 64
espresso_q_threads: 8
espresso_q_time_hr: 12
espresso_s_mem_gb: 64
espresso_s_threads: 6
espresso_s_time_hr: 12
minimap2_mem_gb: 48
minimap2_threads: 10
minimap2_time_hr: 48
split_s_for_c_mem_gb: 4
split_s_for_c_time_hr: 12
visualize_mem_gb: 40
# Command options
use_annotated_junctions_with_minimap2: true
keep_espresso_c_temp: false
use_blast: false
use_alignment_read_groups: false
output_compatible_isoforms: false
output_corrected_sam_files: false
corrected_sam_aligner_window: 400
target_reads_per_espresso_c_job: 400000
# Visualization options
enable_visualization: false
vis_normalize_counts: false
vis_target_gene: ''
vis_minimum_count: 1
vis_descriptive_name: 'ESPRESSO'
# Reference files:
# The snakemake can automatically download and gunzip files if
# a matching url entry is given in the reference_files section below.
# If the entry in the reference_files section ends with .gz then the
# snakemake will gunzip the file.
# **The gtf_name and fasta_name should not end with .gz**
gtf_name: 'gencode.v46.primary_assembly.annotation.gtf'
fasta_name: 'GRCh38.primary_assembly.genome.fa'
# The entries under reference_files should be
# file_name.with.extension:
#   url: 'url_path/to_the/file_name.with.extension'
#
# The 'url:' will be used to download the file and it will be put in
# references/ with the name given on the line above the 'url:'.
# The file will be gunzipped and the .gz removed if needed.
reference_files:
  gencode.v46.primary_assembly.annotation.gtf.gz:
    url: 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/gencode.v46.primary_assembly.annotation.gtf.gz'
  GRCh38.primary_assembly.genome.fa.gz:
    url: 'https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_46/GRCh38.primary_assembly.genome.fa.gz'
# Input samples:
# Each sample name will have a separate column in the abundance.esp output file.
# Replicates can be given as separate sample names
# (sample_1_rep_1, sample_1_rep_2, ...) to have the abundance counted separately.
# Alternatively, replicates can be listed under the same sample name to combine
# the counts in the final output.
samples:
  sample_1_name:
    - fastq: '/path/to/file.fastq'
  sample_2_name:
    - fastq: '/path/to/file.fastq'
# Additional configuration
guppy_bin_path: '/path/to/guppy/bin/'
guppy_gpu: false
# libparasail_so_path: '/path/to/libparasail.so'