Generate Nextflow command to run pipline

Generate Nextflow command to run pipline

Usage

nextflow_cmd(
  workflow = c("assemble", "annotate"),
  path = NULL,
  source = app_sys("nextflow"),
  userAsmbs = FALSE,
  base = run_basename(workflow)
)

Arguments

workflow

Which module to update (default = c("assemble", "annotate"))

path

MitoPilot project directory

source

Nextflow script source. By default, this will be in the `nextflow/` subdirectory of the package installation.

userAsmbs

User supplied assemblies, TRUE/FALSE? (default = FALSE)

base

Run name used for the log file, `<path>/.runs/nextflow/<base>.nextflow.log`.