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Generate and save a reusable cluster config profile

Source: R/generate_config.R
generate_config.Rd

Configure your HPC cluster once and reuse it for every project. Mirrors MitoPilot's generate_config(). Builds a Nextflow config from a generic scheduler template, fills in cluster-level settings, and saves it as a named profile in ribopilot_config_dir(). Afterwards new_project(executor = "<name>") will find and use it automatically.

Usage

generate_config(
  name,
  scheduler = c("slurm", "sge", "pbs", "lsf", "local"),
  container_engine = c("auto", "singularity", "apptainer", "docker"),
  container_cache = NULL,
  container_run_options = NULL,
  queue = NULL,
  walltime = NULL,
  account = NULL,
  cluster_options = NULL,
  penv = "mthread",
  profile_dir = ribopilot_config_dir(),
  interactive = FALSE,
  overwrite = FALSE
)

Arguments

name

Profile name. Saved as config.<name>; pass as executor.

scheduler

Base template: "slurm", "sge", "pbs", "lsf", or "local" (Docker on one machine, the same as executor = "local").

container_engine

"auto" (default) picks singularity for the schedulers and docker for "local". "singularity", "apptainer", and "docker" apply to slurm, sge, pbs, and lsf; "local" always uses Docker.

container_cache

Folder where Singularity or Apptainer keeps the pulled image, shared by every project that uses this profile; it must be visible from the compute nodes. Default: NXF_SINGULARITY_CACHEDIR (or NXF_APPTAINER_CACHEDIR) when set, otherwise a "containers" folder in the reference folder (RIBOPILOT_REF_DIR, see ribopilot_ref_dir()). Pass "" to leave it to Nextflow (the project's work/singularity folder).

container_run_options

Optional extra runOptions for the container engine (any engine), appended to the bind mounts.

queue

Partition / queue name. If NULL, the directive is omitted.

walltime

Per-job walltime, in a form your scheduler accepts (e.g. "24h", "48:00:00"). Many SLURM and PBS sites reject a job that requests no walltime instead of applying a default. If NULL, the directive is omitted and the site default applies.

account

Optional accounting string, folded into clusterOptions.

cluster_options

Optional raw clusterOptions string appended verbatim.

penv

SGE parallel environment (default "mthread").

profile_dir

Directory to save the profile in.

interactive

If TRUE and interactive, prompt for unset values.

overwrite

Overwrite an existing profile (default FALSE).

Value

(invisibly) the path to the saved profile.