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AWS S3 Sync Helper (ctTSO / dragen-tso500-ctdna)

Source: R/s3.R
s3sync_cttso.Rd

Sync only the small, parse-relevant files from a DRAGEN TSO500 ctDNA run. Excludes the large binaries (BAM, gVCF, bigwig etc.) and the pipeline/nextflow logs. Files live deep under Logs_Intermediates/DragenCaller/<sample>/ and Results/<sample>/.

Usage

s3sync_cttso(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.

dryrun

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

Details

Folder-prefix excludes: aws s3 sync filters are ordered and last-match wins, so an "ex" row placed after an "in" row carves a subset back out (e.g. "in", "*Tmb/*" then "ex", "*Tmb/*.tmb.trace.tsv"). The default patterns use this to drop the Logs_Intermediates/ duplicates while keeping the Results/ copy.

Examples

if (FALSE) { # \dontrun{
d1 <- "s3://pipeline-prod-cache-503977275616-ap-southeast-2/byob-icav2/production/analysis"
src <- file.path(d1, "dragen-tso500-ctdna/20260827e81c2a44")
dest <- sub(d1, here::here("nogit"), src)
s3sync_cttso(src, dest, dryrun = TRUE)

# custom: whole Results/ folder except one file (folder-prefix exclude)
pats <- tibble::tribble(
  ~inex, ~pat,
  "ex", "*",
  "in", "*Results/*",
  "ex", "*Results/*_MetricsOutput.tsv"
)
s3sync_cttso(src, dest, pats = pats, dryrun = TRUE)
} # }