Output Files and Directory Structure¶

The pipeline generates multiple outputs at each stage of analysis. Below is a summary of key files and their locations.

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Directory Structure¶

results/
├── qc/
│   ├── *.fastqc.html           # FastQC reports
│   ├── *.fastp.html/json       # Fastp reports
│   └── multiqc_report.html     # Summary report
├── alignments/
│   ├── *.sam                   # Raw alignments
│   ├── *.sorted.bam            # Sorted BAM files
│   └── *.bai                   # BAM index files
├── clipped/
│   └── *.primerclipped.bam     # Primer-removed alignments
├── variants/
│   └── *.vcf                   # Raw variant calls
├── consensus/
│   └── *.fasta                 # Consensus genome sequences
├── phylogeny/
│   ├── alignment.fasta         # MSA file
│   └── *.treefile              # Phylogenetic tree
├── lineage/
│   └── lineage_report.csv      # Pangolin lineage calls
└── qc_consensus/
    └── output/                 # PRESIDENT quality reports

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Output Types¶

Stage	File Type(s)	Description
Quality Control	.html, .json	QC and trimming reports
Mapping	.bam, .bai	Aligned reads, indexed
Primer Clipping	.primerclipped.bam	Primer-trimmed alignments
Variant Calling	.vcf	Raw variant calls
Consensus	.fasta	Consensus genome sequences
Lineage Annotation	.csv	Pangolin lineage table
Phylogenetic Tree	.fasta, .treefile	MSA + tree structure
QC (Consensus)	output/ files	Nucleotide identity, ambiguities

📁 All files are written into structured subdirectories under results/ by default.

You can modify the output paths via nextflow.config or process-specific directives.