fastani

Additional FastANI References

It is possible to add additional references for FastANI in Grandeur.

Directions

The End User can add their own fasta files with 'params.fastani_ref = <path_to_new_reference.fasta>'. For downstream analyses, the name of these fasta files should be "${genus}${species}${accession}" where genus and species are the genus and species of the organism of the fasta file and the accession is any unique identifier (that does not collide with the names of the genomes already included in the workflow). These fasta files can also be compressed with '.gz'.

If there are multiple fasta files to upload, list the full or relative path of each separated by a comma.

nextflow run UPHL-BioNGS/Grandeur -profile docker <other params> --fastani_ref genus_species_genome1.fasta,genus_species_genome2.fasta,genus_species_genome3.fasta

Another option is to provide a file with the paths to each fasta file and read that in with params.fastani_ref_list.

Example file (file_list.txt):

genomes/genus_species_coolorganism.fa
genomes/genus_species_another.fasta
genomes/genus_species_outgroup.fasta.gz

Using on the command line.

nextflow run UPHL-BioNGS/Grandeur -profile docker <other params> --fastani_ref_list file_list.txt

WARNING : The user-supplied reference genomes cannot match the filenames of any of the included genomes and must be unique from each other. Otherwise, there will be a duplicate filename input error.

params.fastani_ref      = "/path/to/genus_species_references.fasta"
params.fastani_ref_list = "/path/to/file/with/names/of/reference/fastas"