Parameters

This document lists the main configuration parameters used by the CholeraSeq pipeline. For full parameter discovery, see nextflow.config.

Required parameters

Parameter Default Description
input null Path to the sample sheet CSV file containing sample metadata and input paths.
outdir null Output directory for pipeline results.

The sample sheet should contain at least sample, fastq_1, and fastq_2. For single-end or assembly input, leave fastq_2 blank.

Reference and alignment parameters

Parameter Default Description
ref_genbank GCF_003063785.full.gbk Path to the reference GenBank file used by snippy and varcodons.py.
global_core_alignment null Path to an existing global core-genome alignment FASTA to merge with cohort sequences.
cohort_core_alignment null Path to an existing cohort core-genome alignment FASTA to merge into a global core alignment.

Quality control and variant calling

Parameter Default Description
min_trim_quality 20 Minimum average base quality for fastp trimming.
min_trim_length 35 Minimum read length after trimming.
min_mapping_quality 20 Minimum mapping quality used by samtools consensus.
min_base_quality 20 Minimum base quality used by samtools consensus.
min_site_coverage 5 Minimum depth required to call a site.
min_allele_fraction 0.75 Minimum allele frequency required to make a variant call.
max_missing_percentage 50 Maximum allowed percentage of missing data in a consensus sequence before it is filtered.
min_parsimony_coverage 0.7 Minimum fraction of non-missing bases required for a variable site to be retained by varcodons.py.

Clustering and tree options

Parameter Default Description
skip_fastbaps true Skip the optional FastBAPS clustering step.
skip_clustering false Skip the clustering and tree inference workflow. This also skips the iqtree tree step.

Reporting and MultiQC

Parameter Default Description
multiqc_config null Custom MultiQC configuration file.
multiqc_logo ${projectDir}/assets/CERI_logo_b.png Optional logo file to include in MultiQC reports.
multiqc_methods_description null Optional YAML or text file with method descriptions for MultiQC.
email null Email address to notify on successful completion.
email_on_fail null Email address to notify if the pipeline fails.
hook_url null Webhook URL for completion notification.

Execution and environment

Parameter Default Description
custom_config_version 'master' nf-core config repository version to use.
config_profile_description null Optional profile description.
config_profile_name null Optional profile name to expose to readers.
max_memory 128.GB Maximum memory limit applied to pipeline processes.
max_cpus 16 Maximum CPU limit for pipeline processes.
max_time 240.h Maximum runtime limit for pipeline processes.

Notes

  • The pipeline is designed for phylogenetic analysis, not for broad genome characterization.
  • It does not perform AMR profiling, MLST, serotyping, or gene presence/absence analysis.
  • The final tree is built from a reference-guided, recombination-masked core-genome SNP alignment.
  • If you want full details of available parameters, inspect nextflow.config and the schema definitions in the repository.