TreeValTinyFullSangerTest.yaml

assembly:
  assem_level: scaffold
  sample_id: grTriPseu1
  latin_name: to_provide_taxonomic_rank
  defined_class: fungi
  assem_version: 1
  project_id: DTOL
reference_file: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa
map_order: length
assem_reads:
  read_type: hifi
  read_data:
    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/pacbio/seqkitPacbio50000.fasta.gz
  supplementary_data: path
hic_data:
  hic_cram:
    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-1000.cram
    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/genomic_data/hic-arima/SUBSET-2000.cram
  hic_aligner: bwamem2
kmer_profile:
  # kmer_length will act as input for kmer_read_cov fastk and as the name of folder in profile_dir
  kmer_length: 31
  profile: /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData
alignment:
  genesets:
    - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/gene_alignment_data/fungi/csv_data/LaetiporusSulphureus.gfLaeSulp1-data.csv
self_comp:
  motif_len: 0
intron:
  size: "50k"
telomere:
  teloseq: TTAGGG
synteny:
  - /nfs/treeoflife-01/resources/nextflow/test-data/resources/treeval/TreeValTinyData/synteny/fungi/LaetiporusSulphureus.fasta
busco:
  lineages_path: /data/tol/resources/busco/latest/
  lineage: fungi_odb10