Launches the self-contained Nextflow pipeline, the same run as the app's Update button. For every taxonomy-locked sample that is Ready to run, one run cleans the reads, assembles, scores, BLASTs, maps coverage, annotates, curates, screens, checks for chimeras, and triages every contig, writing everything back to the database. Run it again (or press Update) only after changing a selection, an option set, or a State.
Usage
run_assembly(
path = ".",
nextflow = "nextflow",
work = file.path(path, "work"),
conda_env = NULL,
ribopilot_src = NULL
)Arguments
- path
Project directory (contains
.sqliteand.config).- nextflow
Path to the
nextflowbinary.- work
Nextflow work directory (default
<path>/work).- conda_env
Optional conda env providing the pipeline tools; its
bin/is prepended to PATH for the run.- ribopilot_src
Path to the RiboPilot package source for the R-script processes (only needed when the package is not installed; defaults to the loaded package location).