This function runs the full CLI pipeline for barcode analysis: FastQC -> PEAR -> Minimap2 -> BAM Stats.
Usage
run_cli_pipeline(
sample_table,
reference,
output_dir = "results",
verbose = TRUE,
log_file = NULL,
create_output_dir = TRUE
)Arguments
- sample_table
Path to samples.csv or a data.frame/tibble containing `sample`, `R1`, and optionally `R2`.
- reference
Path to reference FASTA file.
- output_dir
Directory to write output files. Default: "results".
- verbose
Whether to print progress messages to console. Default: TRUE.
- log_file
File path for logging. If NULL, uses output_dir/pipeline.log. Default: NULL.
- create_output_dir
Whether to create output_dir if it doesn't exist. Default: TRUE.
Value
Invisible list containing:
commands: Character vector of system commands executed
output_dir: Path to output directory
stats: Data frame with BAM statistics
Examples
if (FALSE) { # \dontrun{
# Run with default output directory (./results)
run_cli_pipeline(
sample_table = "samples.csv",
reference = "barcodes.fasta"
)
# Run with custom output directory
run_cli_pipeline(
sample_table = "samples.csv",
reference = "barcodes.fasta",
output_dir = "/path/to/my_results"
)
} # }