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Directory Structures

data/valid Directory Structure

Each validation run creates a timestamped subdirectory. Previous runs are preserved.

data/valid/
├── validated_params.json          # Fixed path — always here for Nextflow -params-file
│
└── run_YYYYMMDD_HHMMSS/           # Per-run output directory
    ├── SampleName_ref.fasta       # Validated reference genome FASTA
    ├── SampleName_mod.fasta       # Validated modified genome FASTA (if provided)
    ├── SampleName_ref_plasmid.fasta  # Reference plasmid (if identified)
    ├── SampleName_mod_plasmid.fasta  # Modified plasmid (if identified)
    ├── SampleName_contig_0.fasta  # Contig files from fragmented assembly (if applicable)
    ├── SampleName_ref.gff         # Validated GFF annotation (if provided)
    ├── validation.log             # Structured JSON log for this run
    ├── report.txt                 # Human-readable validation statistics
    │
    ├── illumina/
    │   ├── SampleName_R1.fastq.gz
    │   └── SampleName_R2.fastq.gz
    │
    ├── ont/
    │   ├── SampleName.fastq.gz    # FASTQ input (converted/copied)
    │   └── SampleName.bam         # BAM input (copied as-is, if provided)
    │
    └── pacbio/
        ├── SampleName.fastq.gz    # FASTQ input (converted/copied)
        └── SampleName.bam         # BAM input (copied as-is, if provided)

File Descriptions

File / Folder Description
validated_params.json Produced by the validation step; loaded by Nextflow via -params-file. Contains all validated file paths and pipeline flags. Always written at data/valid/ (top level) so the Nextflow command never needs updating between runs.
run_YYYYMMDD_HHMMSS/ Timestamped directory for one validation run. All validated files, the log, and the report go here. Previous runs are never overwritten.
*_ref.fasta Validated reference genome FASTA.
*_mod.fasta Validated modified genome FASTA.
*_ref_plasmid.fasta Reference plasmid sequences (if identified).
*_mod_plasmid.fasta Modified plasmid sequences (if identified).
*_contig_N.fasta Individual contig files from a fragmented modified assembly.
*_ref.gff Validated GFF/GTF feature annotation (if provided).
validation.log Structured JSON log for the run (auto-incremented if re-run in same second).
report.txt Human-readable statistics for all validated files.
illumina/ Paired-end Illumina FASTQ reads.
ont/ Nanopore reads — FASTQ and/or BAM depending on input.
pacbio/ PacBio reads — FASTQ and/or BAM depending on input.

data/outputs Directory Structure

After successful pipeline execution, the outputs are organized as follows:

data/outputs
├── fasta_ref_mod       → Results from reference vs modified FASTA comparison (if run_ref_x_mod is set to true in `data/valid/validated_params.json`)
├── illumina            → Short-read (Illumina) mapping results
├── logs/               → Pipeline logs, Nextflow reports, trace data, and process manifest
├── ont                 → Long-read (Oxford Nanopore) mapping results
├── pacbio              → Long-read (PacBio) mapping results
├── tables              → Per-SV csv tables
├── truvari             → Variant comparison results from Truvari (if run_truvari is set to true in `data/valid/validated_params.json`)
└── unmapped_stats      → Summary statistics of unmapped reads for each workflow

Output Documentation

A detailed description of each output subfolder is available in the Output Documentation:

See Also