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nxOscDF5033.yaml
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nxOscDF5033.yaml
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assembly:
assem_level: scaffold
assem_version: 1
sample_id: Oscheius_DF5033
latin_name: to_provide_taxonomic_rank
defined_class: nematode
project_id: DTOL
reference_file: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta
map_order: length
assem_reads:
read_type: hifi
read_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
supplementary_data: path
hic_data:
hic_cram: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/
hic_aligner: minimap2
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
dir: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/
alignment:
data_dir: /lustre/scratch123/tol/resources/treeval/gene_alignment_data/
common_name: "" # For future implementation (adding bee, wasp, ant etc)
geneset_id: "OscheiusTipulae.ASM1342590v1,CaenorhabditisElegans.WBcel235,Gae_host.Gae"
#Path should end up looking like "{data_dir}{classT}/{common_name}/csv_data/{geneset}-data.csv"
self_comp:
motif_len: 0
mummer_chunk: 10
intron:
size: "50k"
telomere:
teloseq: TTAGGG
synteny:
synteny_path: /nfs/treeoflife-01/teams/tola/users/dp24/treeval/TreeValTinyData/synteny/
synteny_genomes: ""
busco:
lineages_path: /lustre/scratch123/tol/resources/busco/v5
lineage: nematoda_odb10