nf-fgsv

Note

This repository is primarily for testing the latest Nextflow features and the workflow is relatively simple.

This is a Nextflow workflow for running fgsv on a BAM file to gather evidence for structural variation via breakpoint detection.

Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with nf-fgsv and beyond.

Set up Environment

Make sure Pixi and Docker are installed.

The environment for this analysis is in pixi.toml and is named nf-fgsv.

To install:

pixi install

Run the Workflow

To save on typing, a pixi task is available which aliases nextflow run main.nf.

pixi run \
    nf-workflow \
        -profile "local,docker" \
        --input tests/data/basic_input.tsv

Available Execution Profiles

Several default profiles are available:

• local limits the resources used by the workflow to (hopefully) reasonable levels
• docker specifies docker containers should be used for process execution
• linux adds --user root to docker runOptions

Inputs

A full description of input parameters is available using the workflow --help parameter, pixi run nf-workflow --help.

The required columns in the --input samplesheet are:

Field	Type	Description
sample	String, no whitespace	Sample identifier
bam	Absolute path	Path to the BAM file for this sample (may be an AWS S3 path)

Parameter files

If using more than a few parameters, consider saving them in a YAML format file (e.g. tests/integration/params.yml).

pixi run \
    nf-workflow \
        -profile "local,docker" \
        -params-file my_params.yml

Outputs

The output directory can be specified using the -output-dir Nextflow parameter. The default output directory is results/. -output-dir cannot be specified in a params.yml file, because it is a Nextflow parameter rather than a workflow parameter. It must be specified on the command line or in a nextflow.config file.

pixi run \
    nf-workflow \
        -profile "local,docker" \
        --input tests/data/basic_input.tsv \
        -output-dir results

Click to toggle output directory structure

results
└── {sample_name}
    ├── {sample_name}_sorted.bam                # Coordinate-sorted BAM file
    ├── {sample_name}_svpileup.txt              # SvPileup breakpoint candidates
    ├── {sample_name}_svpileup.bam              # BAM with SV tags from SvPileup
    ├── {sample_name}_svpileup.aggregate.txt    # Aggregated/merged breakpoint pileups
    └── {sample_name}_svpileup.aggregate.bedpe  # Aggregated pileups in BEDPE format

Output File Descriptions

File	Description
*_sorted.bam	Input BAM sorted by genomic coordinates using samtools sort
*_svpileup.txt	Candidate structural variant breakpoints identified by fgsv SvPileup
*_svpileup.bam	BAM file with SV-related tags added by SvPileup
*_svpileup.aggregate.txt	Merged breakpoint pileups from fgsv AggregateSvPileup
*_svpileup.aggregate.bedpe	Aggregated pileups converted to BEDPE format

Contributing

See our Contributing Guide for development and testing guidelines.