DLBPointon
commented
9 months ago proposed structure:
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
assem_reads:
longread_type: hifi
longread_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/
hic_data: /lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/
supplementary_data: path
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_genome_path: /lustre/scratch123/tol/resources/treeval/synteny/
busco:
lineages_path: /lustre/scratch123/tol/resources/busco/v5
lineage: nematoda_odb10
Description of the bug
Currently there are a few variables which would make no sense to an outside eye.
gevalType being one, this should be replaced with ProjectID or TicketType
Add readType ('hifi','clr','ont','illumina') as new value - to be used in read coverage - see ASCC.
Command used and terminal output
No response
Relevant files
No response
System information
No response