Output section #

The [output] table controls how transformed reads and reporting artefacts are written.

[output]
    prefix = "output"          # required.
    format = "Gzip"             # Raw | Gzip | Zstd | None (default: Raw)
    suffix = ".fq.gz"           # optional override; inferred from format when omitted
    compression_level = 6        # gzip: 0-9, zstd: 1-22; defaults are gzip=6, zstd=5

    report_json = false          # write prefix.json
    report_html = true           # write prefix.html

    output = ["read1", "read2"] # limit which segments become FastQ files
    interleave = false           # emit a single interleaved FastQ
    stdout = false               # stream to stdout instead of files

    output_hash_uncompressed = false
    output_hash_compressed = false

Key	Default	Description
`prefix`	`"output"`	Base name for all files produced by the run.
`format`	`"Raw"`	Compression applied to FastQ outputs. `None` disables FastQ emission but still allows reports.
`suffix`	derived from format	Override file extension when interop with other tooling demands a specific suffix.
`compression_level`	gzip: 6, zstd: 5	Fine-tune compression effort. Ignored for `Raw`/`None`.
`report_json` / `report_html`	`false`	Toggle structured or interactive reports.
`output`	all input segments	Restrict the subset of segments written to disk. Use an empty list to suppress FastQs while still running steps that depend on fragment data.
`interleave`	`false`	Generate a single interleaved FastQ (`{prefix}_interleaved.fq*`).
`stdout`	`false`	Write to stdout. Forces `format = "Raw"`. `Sets interleave=true` if more than one fragment is listed in `output`
`output_hash_uncompressed` / `output_hash_compressed`	`false`	Emit SHA-256 checksums.

Generated filenames follow {prefix}_{segment}{suffix}. Interleaving replaces segment with ‘interleaved’. Demultiplexing adds additional infixes. Checksums use .uncompressed.sha256 or .compressed.sha256 suffixes.

Compression format and suffix are independent: overriding the suffix will not change the actual compression algorithm.

Example output files. #

As above #

The above configuration produces:

output_read1.fq.gz # .fq is the default suffix for raw, .fq.gz for gzip
output_read2.fq.gz
output.html # HTML report

If Interleaved was set #

output_interleaved.fq.gz
output.html # HTML report

No FastQ output #

Set format = "None" or output = [] when you only need reports or tag quantification. A prefix is still required so report files have a stable name.

See also the Report steps reference for producing summaries, and the Demultiplex documentation for how barcode outputs influence file naming.