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Read a Snakemake pipeline configuration file.

Source: R/read-config.R
read_pipeline_config.Rd

Parse a YAML config file from the tRNA sequencing pipeline and return a structured list with sample information, output directory, and FASTA reference path. Relative paths are resolved relative to the config file directory.

Usage

read_pipeline_config(config_path)

Arguments

config_path

Path to a Snakemake config.yaml file.

Value

A list with elements:

  • samples: A tibble with columns sample_id and data_path.

  • output_dir: Resolved path to pipeline output directory.

  • fasta: Resolved path to reference FASTA file.

  • config_dir: Directory containing the config file.

Examples

config <- read_pipeline_config(clover_example("ecoli/config.yaml"))
config$samples
#> # A tibble: 6 × 2
#>   sample_id    data_path         
#>   <chr>        <chr>             
#> 1 wt-15-ctl-01 /data/wt-15-ctl-01
#> 2 wt-15-ctl-02 /data/wt-15-ctl-02
#> 3 wt-15-ctl-03 /data/wt-15-ctl-03
#> 4 wt-15-inf-01 /data/wt-15-inf-01
#> 5 wt-15-inf-02 /data/wt-15-inf-02
#> 6 wt-15-inf-03 /data/wt-15-inf-03
config$output_dir
#> [1] "/home/runner/work/_temp/Library/clover/extdata/ecoli"