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Parameters Reference

Complete reference for all pipeline parameters.

Required Parameters

Core Input/Output

Parameter Type Description Example
--csvFile string Path to input CSV metadata file data/genomes.csv
--outdir string Output directory for results ./results

Required

These parameters must be provided for every pipeline run.

Workflow Selection

Enable specific analysis workflows:

Parameter Type Default Description
--run_busco_core boolean false Run BUSCO using MySQL core database
--run_busco_ncbi boolean false Run BUSCO using NCBI assembly accession (genome mode only)
--run_omark boolean false Run OMArk proteome assessment
--run_ensembl_stats boolean false Generate Ensembl statistics
--run_ensembl_beta_metakeys boolean false Generate Ensembl beta metakeys

Examples

# Run BUSCO only
--run_busco_core

# Run multiple workflows
--run_busco_core --run_omark --run_ensembl_stats

# BUSCO from NCBI
--run_busco_ncbi

Database Connection

Parameters for connecting to Ensembl core databases:

Parameter Type Description Example
--host string Database host server mysql-server.example.com
--port integer Database port 3306
--user_r string Read-only database user readonly_user
--user string Database user with write permissions ensadmin
--password string Database password secret123

Database Access

  • --user_r is sufficient for quality metrics generation
  • --user and --password are only required when applying statistics to the database

Example

nextflow run main.nf \
  --csvFile genomes.csv \
  --run_ensembl_stats \
  --host mysql-ens-sta-5.example.com \
  --port 4686 \
  --user_r ensro

BUSCO Parameters

Mode Selection

Parameter Type Default Options Description
--busco_mode string protein protein, genome, both BUSCO analysis mode
  • protein: Analyze protein sequences from gene predictions
  • genome: Analyze genome assembly directly
  • both: Run both protein and genome modes

Lineage Dataset

Parameter Type Description Example
--busco_dataset string Default BUSCO lineage for all samples vertebrata_odb12

Per-Sample Lineage

You can also specify lineage per sample in the CSV file using the busco_dataset column.

BUSCO Configuration

Parameter Type Default Description
--busco_version string v6.0.0_cv1 BUSCO container image version
--download_path string /nfs/production/flicek/ensembl/genebuild/genebuild_virtual_user/data/busco_data/data_odb12/ Path to BUSCO lineage datasets
--busco_datasets_file string ../data/busco_lineage.json JSON file with available BUSCO lineages
--dump_params string --canonical_only Parameters for sequence dumping

Available BUSCO Lineages

Common lineages (from OrthoDB v12):

Lineage Taxonomic Scope Use For
eukaryota_odb12 All eukaryotes Universal baseline
metazoa_odb12 Animals All animal genomes
vertebrata_odb12 Vertebrates Fish, amphibians, reptiles, birds, mammals
mammalia_odb12 Mammals Human, mouse, cow, etc.
primates_odb12 Primates Human, chimp, gorilla, etc.
aves_odb12 Birds Chicken, zebra finch, etc.
actinopterygii_odb12 Ray-finned fish Zebrafish, medaka, etc.
insecta_odb12 Insects Fly, mosquito, bee, etc.
diptera_odb12 Flies Drosophila, mosquitoes
fungi_odb12 Fungi Yeast, Aspergillus, etc.
viridiplantae_odb12 Plants All plant genomes
embryophyta_odb12 Land plants Arabidopsis, rice, etc.

For the complete list, check the BUSCO datasets file or visit BUSCO website.

Example

# Use vertebrate lineage in protein mode
nextflow run main.nf \
  --csvFile genomes.csv \
  --run_busco_core \
  --busco_mode protein \
  --busco_dataset vertebrata_odb12

# Run both protein and genome modes
nextflow run main.nf \
  --csvFile genomes.csv \
  --run_busco_core \
  --busco_mode both

OMArk Parameters

Parameter Type Default Description
--omamer_database string /nfs/production/flicek/ensembl/genebuild/genebuild_virtual_user/data/omamer_db/LUCA_MinFamSize6_OR_MinFamComp05_A21_k6.h5 Path to OMArk/OMAmer database
--omark_singularity_path string /hps/software/users/ensembl/genebuild/genebuild_virtual_user/singularity/omark.sif Path to OMArk Singularity container

Example

nextflow run main.nf \
  --csvFile proteomes.csv \
  --run_omark \
  --omamer_database /data/omamer/LUCA.h5 \
  --host mysql-server.example.com \
  --user_r ensro

Ensembl Statistics Parameters

Parameter Type Default Description
--enscode string - Path to Ensembl API/modules directory
--bioperl string /bioperl-1.6.924 Path to BioPerl installation
--mysql_ensadmin string /hps/software/users/ensembl/ensw/mysql-cmds/ensembl/ensadmin Path to ensadmin script
--meta_query_file string ../bin/meta.sql SQL query file for metadata
--project string ensembl Project name for metadata
--team string - Team responsible (metakey)

Apply Statistics to Database

Parameter Type Default Description
--apply_ensembl_stats boolean false Insert statistics into the database
--apply_ensembl_beta_metakeys boolean false Insert beta metakeys into the database
--apply_busco_metakeys boolean false Create and load BUSCO metakeys JSON

Database Write Access Required

When using --apply_* parameters, you must provide --user and --password with write permissions.

Example

# Generate statistics only
nextflow run main.nf \
  --csvFile databases.csv \
  --run_ensembl_stats \
  --enscode /nfs/software/ensembl/ENSCODE \
  --host mysql-server.example.com \
  --user_r ensro

# Generate and apply to database
nextflow run main.nf \
  --csvFile databases.csv \
  --run_ensembl_stats \
  --apply_ensembl_stats \
  --enscode /nfs/software/ensembl/ENSCODE \
  --host mysql-server.example.com \
  --user ensadmin \
  --password secret123 \
  --team genebuild

NCBI Download Parameters

For BUSCO NCBI mode:

Parameter Type Default Description
--ncbiBaseUrl string https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/ NCBI API base URL

Example

nextflow run main.nf \
  --csvFile ncbi_assemblies.csv \
  --run_busco_ncbi \
  --busco_dataset vertebrata_odb12

Cache and Cleanup

Parameter Type Default Description
--cacheDir string ./results/cache Directory for caching downloaded files
--cleanCache boolean false Clean cache directory after pipeline completion
--files_latency integer 60 File system latency in seconds

Example

# Keep cache for debugging
nextflow run main.nf \
  --csvFile genomes.csv \
  --run_busco_ncbi \
  --cleanCache false

# Use custom cache location
nextflow run main.nf \
  --csvFile genomes.csv \
  --run_busco_ncbi \
  --cacheDir /scratch/pipeline_cache

Pipeline Info

Parameter Type Default Description
--tracedir string ./results/pipeline_info Directory for pipeline execution reports

The trace directory contains:

  • execution_trace.txt: Task-level execution details
  • execution_timeline.html: Visual timeline of task execution
  • execution_report.html: Resource usage report
  • software_versions.yml: Versions of all software used

Resource Limits

Control maximum resources used by the pipeline:

Parameter Type Default Description
--max_cpus integer - Maximum CPUs per process
--max_memory memory - Maximum memory per process
--max_time time - Maximum time per process

Example

nextflow run main.nf \
  --csvFile genomes.csv \
  --run_busco_core \
  --max_cpus 16 \
  --max_memory 64.GB \
  --max_time 24.h

Advanced Parameters

Hidden Parameters

These are typically auto-configured but can be overridden:

Parameter Type Description
--dbname string Database name (typically from CSV)
--readme string Path to README file

Complete Example

Full pipeline run with all common parameters:

nextflow run main.nf \
  --csvFile input_genomes.csv \
  --outdir /data/results/qc_pipeline \
  --run_busco_core \
  --run_omark \
  --run_ensembl_stats \
  --busco_mode both \
  --busco_dataset vertebrata_odb12 \
  --host mysql-ens-sta-5.ebi.ac.uk \
  --port 4686 \
  --user_r ensro \
  --enscode /nfs/software/ensembl/ENSCODE \
  --cacheDir /scratch/cache \
  --cleanCache true \
  --max_cpus 32 \
  --max_memory 128.GB \
  -profile singularity \
  -resume

Parameter Files

For complex configurations, use a parameter file:

# params.yml
csvFile: "genomes.csv"
outdir: "results"
run_busco_core: true
run_omark: true
busco_mode: "both"
host: "mysql-server.example.com"
port: 3306
user_r: "ensro"
enscode: "/software/ensembl/ENSCODE"
max_cpus: 32
max_memory: "128 GB"

Run with:

nextflow run main.nf -params-file params.yml -profile docker

Next Steps