Output section #

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

[output]
    prefix = "output"          # required.
    ix_separator = "_"          # optional separator between prefix, infixes, and segments. Defaults to '_'
    compression_threads = 5        # (optional) number of threads to use for compressing gzip data

Key	Default	Description
`prefix`	`"output"`	Base name for all files produced by the run.
`ix_separator`	`"_"`	Separator inserted between `prefix`, any infix (demultiplex labels, inspect names, etc.), and segment names.
`compression_threads`	auto	if using gzip compression, or bam output, how many thread should be used for compression. See threading

Generated filenames join these components with ix_separator (default _), e.g. {prefix}_{segment}{suffix}. Interleaving replaces segment with interleaved; demultiplexing adds per-barcode infixes before the segment. Checksums use .uncompressed.sha256 or .compressed.sha256 suffixes.

For actual output writing, see the following steps:

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

Note that a pipeline requires at least one output file generating job, i.e one of the above or for example:

Named pipe outputs #

Output files may be (preexisting) named pipes (FIFOs).

Overwrite protection #

If any output file already exists, fastqrab will refuse to overwrite them.

Except when the incompletion marker (see below) is present.

(In-)Completion marker #

Every run writes {prefix}.incompleted in the output directory before any other file handles are opened. The file is deleted once processing finishes, so its presence later indicates an interrupted run.

Because the marker predates other outputs, reruns detect its presence and permit overwriting prior artefacts without manual cleanup.

If the process aborts for any reason, the marker stays behind.