Skip to content

Latest commit

 

History

History
49 lines (41 loc) · 5.38 KB

config.md

File metadata and controls

49 lines (41 loc) · 5.38 KB

Configuration files

Nextflow configuration is controlled by .config files, which specify parameters and other options used in executing the pipeline.

All configuration files used in the pipeline are stored in the configs directory. To configure a specific pipeline run, copy the appropriate config file for that pipeline mode (e.g. run.config) into the launch directory, rename it to nextflow.config, and edit it as appropriate. That config file will in turn call other, standard config files included in the configs directory.

The rest of this page describes the specific options present in each config file, with a focus on those intended to be copied and edited by users.

Run workflow configuration (configs/run.config)

This configuration file controls the pipeline's main RUN workflow. Its options are as follows:

  • params.mode = "run" [str]: This instructs the pipeline to execute the core run workflow.
  • params.ont = false [bool]: Run the pipeline with Illumina data (ONT data is under development but not yet fully supported)
  • params.base_dir [str]: Path to the parent directory for the pipeline working and output directories.
  • params.ref_dir [str]: Path to the directory containing the outputs of the index workflow.
  • params.sample_sheet [str]: Path to the sample sheet used for the pipeline run.
  • params.adapters [str]: Path to the adapter file for adapter trimming (default ref/adapters.fasta.
  • params.n_reads_profile [int]: The number of reads per sample to run through taxonomic profiling (default 1 million).
  • params.bt2_score_threshold [float]: The length-normalized Bowtie2 score threshold above which a read is considered a valid hit for a host-infecting virus (typically 15 or 20).
  • params.bracken_threshold [int]: Minimum number of reads that must be assigned to a taxon for Bracken to include it. (Default 10, can be lowered for testing on very small datasets)
  • params.host_taxon [str]: Host taxon to use for host-infecting virus identification with Kraken2. (default "vertebrate")
  • random_seed [str]: Random seem for non-deterministic processes. Should generally be blank ("") in non-test settings.
  • params.blast_db_prefix [str]: The prefix for the BLAST database to use for host-infecting virus identification (should match the index workflow's params.blast_db_name).
  • params.blast_viral_fraction [float]: The fraction of putative host-infecting virus reads to validate with BLASTN (0 = don't run BLAST).
  • params.blast_min_frac [float]: Keep BLAST hits whose bitscore is at least this fraction of the best bitscore for that query. (default 0.9)
  • params.blast_max_rank [int]: Keep BLAST hits whose dense bitscore rank for that query is at most this value.
  • process.queue [str]: The AWS Batch job queue to use for this pipeline run.

Index workflow (configs/index.config)

  • params.mode = "index" [str]: This instructs the pipeline to execute the index workflow.
  • params.base_dir [str]: Path to the parent directory for the pipeline working and output directories.
  • params.taxonomy_url [str]: URL for the NCBI taxonomy dump to be used in index generation.
  • params.virus_host_db_url [str]: URL for Virus-Host DB.
  • params.human_url [str]: URL for downloading the human genome in FASTA format, which is used in index construction for contaminant screening.
  • params.genome_urls [list(str)]: URLs for downloading other common contaminant genomes.
  • params.ssu_url [str]: URL for the SILVA SSU reference database, used in ribosomal classification.
  • params.lsu_url [str]: URL for the SILVA LSU reference database, used in ribosomal classification.
  • params.host_taxon_db [str]: Path to a TSV mapping host taxon names to taxids (default: ref/host-taxa.tsv.
  • params.contaminants [str]: Path to a local file containing other contaminant genomes to exclude during contaminant filtering (default ref/contaminants.fasta.gz.
  • params.adapters [str]: Path to the adapter file for adapter masking during reference DB generation (default ref/adapters.fasta.
  • params.genome_patterns_exclude [str]: Path to a text file specifying string patterns to hard-exclude genomes during viral genome DB generation (e.g. transgenic sequences) (default ref/hv_patterns_exclude.txt.
  • params.kraken_db [str]: Path to pre-generated Kraken2 reference database (we use the Standard database by default)
  • params.blast_db_name [str]: The name of the BLAST database to use for optional validation of taxonomic assignments (should match the run workflow's params.blast_db_prefix).
  • params.ncbi_viral_params [str]: Parameters to pass to ncbi-genome-download when generating viral genome DB. Must at a minimum specify --section genbank or --section refseq.
  • params.virus_taxid [int]: The NCBI taxid for the Viruses taxon (currently 10239).
  • params.viral_taxids_exclude [str]: Space-separated string of taxids to hard-exclude from the list of host-infecting viruses. Currently includes phage taxa that Virus-Host DB erroneously classifies as human-infecting.
  • params.host_taxa_screen: Space-separated list of host taxon names to screen for when building the viral genome database. Should correspond to taxa included in params.host_taxon_db.