Updating the nextflow config file

1. Locate the config file in the File Browser.
2. Double-click on nextflow.config to edit
3. Update the relevent lines (see below), save and close.

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For the taxonomy module

The taxonomy module uses the maxThree database.

maxThree has two parts:

• params.fastanidbpath, the reference genome sequences (ending .fasta) and
• params.fastanireflistpath, the names of the reference genomes grouped in files by Genus.

Be sure the update both:

params.fastanidbpath = "/file_path/fna_YYYY-MM-DD/*"

params.fastanireflistpath = "/file_path/fna_ref_lists_YYYY-MM-DD/*"

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For the phylogeny module

The phylogeny module uses the maxOne database.

The location of the database is specified here:

params.lsbsrrefgenomefasta = "/file_path/fasta_YYYY-MM-DD/"

genomes must end in .fasta.

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Paths to kraken2 databases

kraken2 databases can either be made or a pre-built one can be downloaded. The three processes of the Core Tool that use kraken2 databases are:

• kdbpath is used to determine the Genus of each query strain,
• kdb_minikraken_path is only run if the isolate is of an unexpected Genus, and
• kdb_reads_path determines if contamination is present in the raw reads.

Multiple kraken2 databases can be specified using:

params.kdbpath = "/file_path/database_name_YYYYMMDD"

params.kdb_minikraken_path = "/file_path/database_name_YYYYMMDD"

params.kdb_reads_path = "/file_path/database_name_YYYYMMDD"

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