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config.yml
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49 lines (39 loc) · 1.09 KB
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# Location of BacQuerya_processing repository relative to the Snakefile
BactQuerya_location: .
# multiprocessing option
n_cpu: 4
# options for extract_entrez_information
extract_entrez_information:
accession_file: SPARC_accessions.txt
email: empty
assembly: assembly-stats
gff: annotation
genome: genome
# options to extract sequence reads
extract_read_metadata:
accession_file: test/read_accessions.txt
# options for single_meryl_dbs
single_meryl_dbs:
single_files: meryl_single_files
assembly_txt_file: meryl_single_files/assembly_str.txt
# options for merge_single_meryl_dbs
merge_single_meryl_dbs:
merged_db_folder: meryl_merged_files
# options for run_merqury
run_merqury:
merqury_output: merqury_output
# options for extract_assembly_stats
extract_assembly_stats:
index_no: 0
# options for extract_genes
extract_genes:
index_no: 0
# options for index_isolate_attributes
index_isolate_attributes:
index: sparc_isolate_index
# options for index_gene_features
index_sequences:
kmer_length: 31
gene_type: gene
elasticSearchIndex: sparc_project_genes
assembly_type: assembly