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

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:

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

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¶

Contributing¶

See our Contributing Guide for development and testing guidelines.