Pipeline Inputs

This page documents all input parameters for the pipeline.

Main workflow parameters

--input

Type: string | Required | Format: file-path

Path to a tab-separated values (TSV) sample sheet describing the samples to analyze. The file must have a header row with the following required columns:

• sample: a unique sample identifier containing no whitespace; used as the meta.id that names per-sample outputs.
• bam: path to an existing BAM file for the sample (must end in .bam).

See schemas/input_schema.json for the full validation rules.

Pattern: .*.tsv$

This pipeline was built with Nextflow. Documentation generated by nf-docs v0.4.0 on 2026-06-03 18:53:33 UTC.