config_T2T.yaml

### Pipeline options

# Input parameters
input_format: "pod5" #pod5 or bam (aligned bam)
basecalling_mode: "methylation" #methylation or basic
variant_calling_mode: "germline" #germline or somatic

# Output parameter
output_dir: "path/to/data_output/"

# Select which parts of the pipeline should be run
steps:
  basecalling: true
  alignment: true
  differential_methylation_sample: true
  differential_methylation_condition: true
  snv_calling: true
  sv_calling: true
  phasing: true
  cnv_calling: true

# Path to design file
design: "path/to/my_design.tsv"

# References information
references:
  genome: "/mnt/beegfs/database/bioinfo/Index_DB/Fasta/Ensembl/T2T-CHM13v2.0/Homo_sapiens-GCA_009914755.4-unmasked.fa"
  genome_fai: "/mnt/beegfs/database/bioinfo/Index_DB/Fasta/Ensembl/T2T-CHM13v2.0/Homo_sapiens-GCA_009914755.4-unmasked.fa.fai"
  genome_snpEff: ""
  dbnsfp: ""
  clinvar: "/mnt/beegfs/database/bioinfo/Index_DB/ClinVar/liftover_GRCh38_to_T2T-CHM13v2.0/chm13v2.0_ClinVar20220313.vcf.gz"
  genome_annotsv: ""
  annotsv: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/ANNOTATIONS/AnnotSV_annotations/"
  code_symbol_conversion: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/REFERENCES/DMR/T2T-CHM13v2.0/correspondance_table_ENST_ENSG.tsv"
  fastq_screen_conf: "/mnt/beegfs/database/bioinfo/Index_DB/Fastq_Screen/0.15.3/minimap2/fastq_screen.conf"
  chromosomes: ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20', '21', '22', 'X', 'Y']

# DMR references
Alu: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/REFERENCES/DMR/T2T-CHM13v2.0/Alu_ucsc_T2T.bed"
CpG: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/REFERENCES/DMR/T2T-CHM13v2.0/CpG_ucsc_T2T.bed"
Transcript: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/REFERENCES/DMR/T2T-CHM13v2.0/Transcript_ucsc_T2T.bed"

# Basecalling parameters
dorado_basecaller:
  model: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/MODELS/dorado/model_r10/dna_r10.4.1_e8.2_400bps_sup@v5.0.0" # Dorado basecaller model v5.0.0 SUP for R10
  model_meth: "/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/MODELS/dorado/model_r10/dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v2"
  meth_type: ["5mCG","5hmCG"] #mandatory if basecalling is set to false.

# Reads filtering parameters
reads_filtering:
  min_read_length: 1000 #Only >= 1000 bp long reads will be kept for mapping
  min_quality_score: 10 #Only reads with base quality score >= 10 will be kept for mapping

# Germline SNV calling parameters
clair3:
  model: ["/mnt/beegfs/database/bioinfo/bigr_long-reads_bulk/MODELS/rerio/clair3_models/r1041_e82_400bps_sup_v500"] # Rerio Clair3 model for data obtained using Dorado basecaller model v5.0.0 SUP for R10

# Somatic SNV parameters
clairs:
  model: "ont_r10_dorado_sup_5khz" # R10 model 

# SNV annotation parameters
snpsift:
  keep_only_pass: true #Filter VCF output from the variant caller to keep only variants annotated as FILTER="PASS" before running the annotation and filtering steps
  filters: ["( QUAL >= 10 )", "( QUAL >= 15 )"] # will output 2 files (1 by filter)

# SNV graph parameters
maftools:
  genes_of_interest: "path/to/my_genes_list.txt"

# CNV parameters
spectre:
  blacklist: ""