annotation_min_mapq:
  10
min_cpg:
  5
min_diff:
  0.3
min_cov:
  5
rawsuffixregex:
  first:  '(_1|_R1_[0-9]+)\.(fastq|fq)(\.gz)?'
  second: '(_2|_R2_[0-9]+)\.(fastq|fq)(\.gz)?'
target_files: [
  'dmr/annotated-dmrs.csv',
  'qc/multiqc_report.html',
  'qc/methylation_metrics.csv',
  'segmentation/umr-lmr-all.csv'
]
dmr_tools: [
  'bsseq',
  #'camel',
  'metilene'
]
promoter_tss_distances: [
  -1000,
  1000
]
annotation_allowed_biotypes: [
  # protein coding genes
  'protein_coding',
  # lncRNA
  'non_coding',
  '3prime_overlapping_ncRNA',
  'antisense',
  'lincRNA',
  'retained_intron',
  'sense_intronic',
  'sense_overlapping',
  'macro_lncRNA',
  'bidirectional_promoter_lncRNA',
  # miRNA
  'miRNA'
]
repeat_masker_links: {
  'annotation/repeat-masker-hg38.csv.gz': 'https://uni-muenster.sciebo.de/s/LwMik3kKY83oVT0/download',
  'annotation/repeat-masker-hg19.csv.gz': 'https://uni-muenster.sciebo.de/s/tFPOT7weAc5eGLG/download'
}
methylation_rate_on_chromosomes: []
methylseekr_pmd_chromosome: '22'
methylseekr_fdr_cutoff: 5
methylseekr_methylation_cutoff: 0.5
qualimap_memory_gb:
  32
bsseq_local_correct:
  FALSE
