AWS S3 Sync Helper

Syncs the parse-relevant DRAGEN outputs (any pipeline, incl. BCLConvert Reports/) from src to dest. Include patterns come from the tool schemas (see nemo::wf_sync_patterns()), followed by DRAGEN_SYNC_EXCLUDE.

Usage

s3sync(src, dest, pats = NULL, dryrun = FALSE)

Arguments

src

(character(1))
S3 source path.

dest

(character(1))
Local destination path.

pats

(tibble())
Patterns tibble with inex ("in" or "ex") and pat (pattern) columns. If NULL and workflow is given, the workflow's schema-derived patterns are used (see wf_sync_patterns()); if both are NULL, everything is excluded.

dryrun

(logical(1))
If TRUE, passes --dryrun to aws s3 sync so operations are displayed without being executed.

Examples

if (FALSE) { # \dontrun{
src <- "s3://my-awesome-bucket/path/to/run1"
dest <- sub("s3:/", "~/s3", src)
s3sync(src, dest, dryrun = TRUE)

# inspect what would be pulled down
nemo::wf_sync_patterns("dragen")

# override with your own patterns
pats <- tibble::tribble(
  ~inex, ~pat,
  "ex", "*",
  "in", "*.mapping_metrics.csv"
)
s3sync(src, dest, pats)
} # }