ChoCallate 🍫

ChoCallate (Chorus of Callers) - a Nextflow pipeline for consensus-based variant calling.

ChoCallate runs several variant callers and applies configurable consensus rules to produce high-confidence SNVs and INDELs. It addresses a critical challenge in variant calling: individual variant callers can produce different results for the same genomic data, leading to uncertainty in variant identification. By implementing a consensus-driven approach, ChoCallate combines results from multiple state-of-the-art variant callers and applies configurable consensus rules to generate reliable, high-quality variant calls.

Requirements

• Linux (tested). macOS/Windows are not currently tested.
• Conda (Miniconda/Anaconda) or Mamba
• Git
• Nextflow

Installation

git clone --depth 1 https://github.com/alermol/ChoCallate.git
cd ChoCallate
conda env create -y -f environment.yaml
conda activate ChoCallate

Optional verification and cleanup:

cd test_run
bash run_test.sh
bash cleanup.sh

Docker

ChoCallate is available as a Docker image on DockerHub. For a fuller walkthrough, see the Wiki: Installing ChoCallate.

docker pull alermol/chocallate:latest

Mount your run directory to /workspace and run:

docker run --rm \
  -u "$(id -u):$(id -g)" \
  -v "${PWD}/input_data:/workspace" \
  -w /workspace \
  alermol/chocallate:latest \
  -params-file config.yaml

Outputs will be written to the configured outdir (default: ChoCallate_output) inside input_data.

Usage

ChoCallate is configured via a Nextflow params YAML file. Start from the template.

cp assets/templates/config.yaml my_run.yaml

Minimum set of parameters in my_run.yaml:

• samples_tsv: input samples TSV (formats below)
• reference_genome: reference FASTA (plain or bgzip-compressed)
• reference_index_dir: path to directory with index files for reference genome

After configuration is complete you can run the ChoCallate

nextflow run main.nf -params-file my_run.yaml

Inputs

• Reads: FASTQs (input_format: "fastq") or a pre-aligned BAM (input_format: "bam"). If you provide a BAM, mapping is skipped.
• Reference genome: Plain or bgzipped FASTA file.
• Indexes of reference genome: All indexes required by the selected mapper/callers.
• Tip: Use absolute paths for inputs.

samples_tsv formats:

• FASTQ + paired-end (reads_type: "pe"): sample_id<TAB>R1<TAB>R2
• FASTQ + single-end (reads_type: "se"): sample_id<TAB>R1
• FASTQ + mixed (reads_type: "mx"): sample_id<TAB>R1<TAB>R2<TAB>U (Bowtie2 mapping only)
• BAM (input_format: "bam"): sample_id<TAB>bam_path

Outputs

Published outputs are written to outdir (default: ChoCallate_output), including standard Nextflow reports:

• pipeline_report.html
• timeline_report.html
• trace.txt

Consensus outputs depend on output.type and output.format:

• Per-sample: <outdir>/per_sample/<sample_id>/consensus.bcf (default) or consensus.vcf.gz
• Single merged: <outdir>/consensus.bcf or <outdir>/consensus.vcf.gz

Additional documentation

• Wiki home: ChoCallate Wiki
• Install: Installing ChoCallate
• Quick start / config & CLI: CLI Reference
• Outputs: Output Structure

Contribution

See CONTRIBUTING.md

License

MIT

Development roadmap

See Development Roadmap for planned container support and additional callers/mappers.