Output Documentation¶

This section provides detailed documentation for all pipeline outputs generated by the EFSA pipeline.

Overview¶

After running the Nextflow pipeline, outputs are organized in the data/outputs/ directory. Each subfolder contains results from different analysis workflows.

Output Categories¶

Whole-Genome Assembly Comparison with SyRI¶

Reference vs Modified FASTA - Results from comparing reference and modified genome assemblies using SyRI and other tools

Short-Read Analysis¶

Short-Read Processing Pipeline Results (Illumina) - Short-read mapping results including BAM files, VCF variants, and coverage statistics

Long-Read Analysis¶

Long-Read Processing Pipeline Results (PacBio & Oxford Nanopore) - Long-read mapping results from PacBio and Oxford Nanopore sequencing

Variant Analysis with Truvari¶

VCF Comparison with Truvari - Structural variant benchmarking and comparison results

Quality Metrics¶

Unmapped Statistics - Summary statistics of unmapped reads for each workflow
Logs - Pipeline execution logs and command history

Output Directory Structure¶

data/outputs/
├── fasta_ref_mod/      → Reference vs modified comparison (if run_ref_x_mod is set to true in `data/valid/validated_params.json`)
├── illumina/           → Short-read mapping results
├── ont/                → Oxford Nanopore results
├── pacbio/             → PacBio results
├── truvari/            → Variant comparison results (if run_truvari is set to true in `data/valid/validated_params.json`)
├── unmapped_stats/     → Unmapped read statistics
└── logs/               → Execution logs, trace data, and process manifest

Output Type	Description	Documentation
Genome Comparison	SyRI structural variant analysis	fasta-ref-mod.md
Short Reads	Illumina mapping and variants	illumina.md
Long Reads	PacBio/ONT mapping	long-reads.md
SV Comparison	Truvari benchmarking	truvari.md
QC Metrics	Unmapped read statistics	unmapped-stats.md
Logs	Command logs and metadata	logs.md