Command line

Commands

seqproc validate <geometry>
seqproc explain <geometry>
seqproc run [OPTIONS]

Command	Purpose
`validate`	Parse, compile, and semantically validate a geometry without reading FASTQ data.
`explain`	Print normalized EFGDL and the compiled geometry representation.
`run`	Process one single-end or paired-end FASTQ input.

The old flag-only form is accepted for one compatibility cycle, but new workflows should use seqproc run.

Required run inputs

--geom and --file1 are required. Supply --file2 for paired-end input. Output arguments are optional syntactically, but an omitted primary output is discarded. Use --out1 and, for two-output geometries, --out2 explicitly.

seqproc run --geom protocol.geom --file1 R1.fastq --out1 clean_R1.fastq

Parallel execution and ordering

--threads N selects the transform worker count. Unordered execution is the default. --preserve-order keeps records in input order with a bounded reorder buffer while transformations remain parallel.

The staged pipeline is enabled automatically for ordered output. It can be requested for unordered processing with --staged-pipeline; this can help expensive geometries, while the normal worker path is often better for cheap ones. Advanced controls are:

--batch-size N
--queue-capacity N
--max-in-flight-batches N

Treat these as workload-specific tuning controls and benchmark before changing their defaults.

Additional geometry arguments

One or more values supplied with --additional fill positional placeholders such as $0 in a geometry. This lets a shared geometry select a whitelist or mapping file at invocation time.

bc = filter_within_dist(b[8], $0, 1)

seqproc run --geom protocol.geom --additional barcodes.txt \
  --file1 reads.fastq.gz --out1 clean.fastq.gz

Output and reporting options

--unassigned1 and --unassigned2 retain records rejected by the main graph.
--demux-map, --demux-label, and --demux-out-dir route accepted reads by sample barcode.
--summary FILE writes a versioned JSON run report.
--statistics-level basic|detailed controls summary detail.

Compression options

--gzip-level 0..9 controls gzip compression for .gz outputs (default 3).
--parallel-gzip emits concatenated gzip members compressed by transform workers.
--parallel-gzip-stream emits one logical gzip member using a bounded compression pool.
--accelerated-gzip-input selects the speculative gzip decoder.

See compressed I/O before enabling the parallel backends, because their thread accounting and interoperability differ.

The executable is the authoritative reference for the installed revision:

seqproc run --help