Usage

This page explains how to run the CERI-KRISP/CholeraSeq pipeline, what inputs it requires, and how to configure a typical analysis.

What CholeraSeq does

CholeraSeq is a Nextflow DSL2 pipeline for Vibrio cholerae outbreak phylogenetics. It processes either raw Illumina reads or FASTA assemblies, performs QC and reference-based variant calling, generates a recombination-masked core alignment, and infers a tree with iqtree.

For a detailed explanation of workflow stages, see workflow.md.

Required inputs

Sample sheet

CholeraSeq requires an input sample sheet in CSV format with a header row. Required columns are:

  • sample
  • fastq_1
  • fastq_2

Each row can represent:

  • paired-end reads (fastq_1 and fastq_2 present)
  • single-end reads (fastq_1 present, fastq_2 blank)
  • an assembly or contig FASTA (fastq_1 contains a FASTA path, fastq_2 blank)

Example sample sheet:

sample,fastq_1,fastq_2
SRR8364252,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR836/002/SRR8364252/SRR8364252_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR836/002/SRR8364252/SRR8364252_2.fastq.gz
SRR771360,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR771/SRR771360/SRR771360.fastq.gz,
AHGB01000000.1,https://github.com/CERI-KRISP/CholeraSeq/raw/b0beafcc6c1315e2782667f0306b10f8b3b7e09a/resources/test_fastas/AHGB01.fasta,

Reference genome

The pipeline uses a GenBank reference for mapping and variant extraction. The default reference is GCF_003063785.full.gbk and can be overridden with --ref_genbank.

Running the pipeline

Example command

nextflow run CERI-KRISP/CholeraSeq \
  -profile docker \
  --input /path/to/samplesheet.csv \
  --outdir results

Test run

A built-in test profile is available for validation:

nextflow run CERI-KRISP/CholeraSeq -profile test,docker --outdir test_output

Use a params file

To reuse the same configuration across multiple runs, provide a parameter file:

nextflow run CERI-KRISP/CholeraSeq -profile docker -params-file params.yaml

Example params.yaml:

input: ./samplesheet.csv
outdir: ./results/
ref_genbank: ./resources/reference/GCF_003063785.full.gbk
skip_fastbaps: true

Reproducibility

Specifying a pipeline release tag ensures the same code version is used:

nextflow run CERI-KRISP/CholeraSeq -r 1.2.0 -profile docker --input samplesheet.csv --outdir results

Output locations

The pipeline writes results into the specified --outdir and creates a work/ directory in the current working directory. Nextflow also writes log and metadata files such as .nextflow_log.

Nextflow command-line options

Note: these options are part of Nextflow and use a single hyphen. Pipeline parameters use double hyphens.

-profile

Choose a configuration profile for software execution. Common pipeline-supported profiles include:

  • docker
  • singularity
  • podman
  • conda
  • test

Example:

nextflow run CERI-KRISP/CholeraSeq -profile test,docker --outdir test_output

-resume

Resume a previous run using cached results when input files and parameters are unchanged.

-params-file

Provide a YAML or JSON file with pipeline parameters.

-c

Use this to load a custom Nextflow config file (typically for cluster or resource settings), not for pipeline parameters.

Key parameters

See parameters.md for the full parameter reference. Common settings include:

  • input: path to the sample sheet
  • outdir: output directory
  • ref_genbank: reference GenBank file
  • global_core_alignment: input global core alignment file
  • cohort_core_alignment: input cohort core alignment file
  • skip_fastbaps: skip FastBAPS clustering
  • skip_clustering: skip the clustering and tree workflow
  • max_missing_percentage: missing-data filter threshold

Profiles and containers

This pipeline supports containerized execution through Docker, Singularity, Podman, and Conda. For reproducibility, use Docker or Singularity whenever possible.

If your environment requires a custom cluster profile, test it with -c and consult nf-core/configs.

Getting help

If you encounter errors, inspect .nextflow_log and the generated pipeline_info/ reports.