Tidy workflow output files

Discovers and tidies files under in_dir for the given workflow, writing results to output_dir in the requested format.

Usage

cli_nemo_tidy(
  workflow,
  in_dir,
  output_dir,
  out_format,
  input_id = NULL,
  output_id = NULL,
  prefix_include = FALSE,
  dbdrv = NULL,
  dbname = NULL,
  dbuser = NULL,
  include = NULL,
  exclude = NULL
)

Arguments

workflow

(character(1))
Workflow name passed to nemoverse_wf_dispatch().

in_dir

(character(1))
Input directory to search.

output_dir

(character(1) or NULL)
Output directory. Required unless out_format is "db".

out_format

(character(1))
Output format. One of "parquet", "tsv", "csv", "rds", or "db".

input_id

(character(1) or NULL)
Input run identifier.

output_id

(character(1) or NULL)
Output run identifier.

prefix_include

(logical(1))
If TRUE, prepend an input_prefix column to each tidy table.

dbdrv

(DBIDriver or NULL)
DBI driver object (e.g. RPostgres::Postgres()). Required when out_format is "db".

dbname

(character(1) or NULL)
Database name. Required when out_format is "db".

dbuser

(character(1) or NULL)
Database user. Required when out_format is "db".

include

(character(n) or NULL)
Tool parser names to include. NULL includes all.

exclude

(character(n) or NULL)
Tool parser names to exclude. NULL excludes none.

Examples

path <- system.file("extdata/tool1", package = "nemo")
out <- tempfile()
res <- cli_nemo_tidy(
  workflow = "workflow1", in_dir = path, output_dir = out,
  out_format = "parquet", input_id = "run1"
)
#> [2026-07-28T09:32:41UTC] nemo INFO: Tidying dir: /home/runner/miniconda3/envs/pkgdown_env/lib/R/library/nemo/extdata/tool1
#> [2026-07-28T09:32:42UTC] nemo INFO: Tidy results written to dir: /tmp/RtmpLFaYvY/file1152df2f982