Samplesheet Format

The samplesheet is a CSV file defining input samples for the Nextflow pipeline.

Basic Format

sample,bam,bai
sample1,/path/to/sample1.bam,/path/to/sample1.bam.bai
sample2,/path/to/sample2.bam,
sample3,/path/to/sample3.bam,/path/to/sample3.bam.bai

Columns

Column	Required	Description
sample	Yes	Sample identifier (used in output filenames)
bam	Yes	Path to BAM file
bai	No	Path to BAM index (auto-discovers .bam.bai or .bai)
suffix	No	Per-sample output suffix

BAI Auto-Discovery

If bai column is empty, the pipeline checks for:

1. <bam>.bai (e.g., sample.bam.bai)

2. <bam_without_extension>.bai (e.g., sample.bai)

!!! tip Leave the bai column empty to use auto-discovery.

Per-Sample Suffix

For samples with multiple BAM types:

sample,bam,bai,suffix
sample1,/path/to/sample1.duplex.bam,,-duplex
sample1,/path/to/sample1.simplex.bam,,-simplex
sample1,/path/to/sample1.unfiltered.bam,,-unfiltered

Output files: sample1-duplex.maf, sample1-simplex.maf, sample1-unfiltered.maf

Related

• Parameters — All pipeline options

• Examples — Common usage patterns

• Troubleshooting — Common issues