Workflows

This page documents all workflows in the pipeline.

Contents

• (entry) (entry point)

(entry)

Entry workflow

Defined in main.nf:35

Detect structural-variant breakpoints from aligned reads using fgsv. The --input sample sheet provides one sample identifier and bam path per row (see the --input parameter for the full column specification). Every per-sample output — the sorted BAM, SvPileup BAM and text, aggregated breakpoints, and BEDPE — is published via the sample_outputs topic into a directory named after the sample's meta.id. For each sample the workflow runs: 1. COORDINATE_SORT — coordinate-sort the input BAM with samtools. 2. SV_PILEUP — gather read-level evidence for structural variants (fgsv SvPileup). 3. AGGREGATE_SV_PILEUP — merge pileups that likely support the same breakpoint. 4. AGGREGATE_SV_PILEUP_TO_BEDPE — convert the aggregated breakpoints to BEDPE.

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