name: run_fimo
task_type: fimo

debug: true

paths:
  input_csv: dpacman/data_files/processed/fimo/remap2022_crm_fimo_input.csv
  json_dir: dpacman/data_files/raw/genomes/hg38
  input_fasta_outer_dir: dpacman/data_files/processed/fimo/chrom_inputs
  fimo_outdir: dpacman/data_files/processed/fimo/fimo_out
  seq_fasta: to_scan.fa
  bg_model: bg_model.txt

meme:
  fimo_bin: /vast/projects/pranam/lab/shared/meme/bin/fimo
  fasta_get_markov: /vast/projects/pranam/lab/shared/meme/libexec/meme-5.5.8/fasta-get-markov
  jaspar_motif_file: /vast/projects/pranam/lab/shared/meme-5.5.8/tests/common/JASPAR_CORE_2014_vertebrates.meme

fimo:
  thresh: 1e-2
  thresh_mode: q
  max_stored: 1000000
  njobs: 64

chroms: [1]
all_caps: true