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Collect selected Cell Ranger files into per-sample folders

TS_collect_cellranger_files.Rd

Copies selected Cell Ranger files into a transfer-friendly destination directory. Each sample receives its own folder. Filtered matrix filenames are kept unchanged for Seurat compatibility, and unfiltered V(D)J all_contig* files are renamed with the sample ID as a prefix. Per-sample V(D)J folders are intentionally not used because they contain filtered contig outputs.

Usage

TS_collect_cellranger_files(
  input_dir,
  dest_dir,
  sample_regex = NULL,
  overwrite = FALSE,
  confirm = interactive(),
  execute = TRUE,
  strict = TRUE,
  ...
)

Arguments

input_dir

Character scalar. Project or Cell Ranger output directory to search.

dest_dir

Character scalar. Destination directory for collected files.

sample_regex

Optional regular expression used to extract sample names. See TS_find_cellranger_samples().

overwrite

Logical. If FALSE, existing destination files cause an error before copying starts.

confirm

Logical. If TRUE, ask for confirmation before copying.

execute

Logical. If FALSE, return the planned copy operations without creating directories or copying files.

strict

Logical. If TRUE, existing raw V(D)J directories must contain all requested all_contig* files. If FALSE, missing V(D)J files are skipped and recorded in the returned plan.

...

Additional arguments passed to TS_find_cellranger_samples(), such as matrix_dir_names or vdj_dir_names.

Value

Invisibly returns the copy plan tibble.

Examples

project <- file.path(tempdir(), "cellranger_project_collect")
matrix_dir <- file.path(project, "sampleA", "cellranger_outs", "filtered_feature_bc_matrix")
dir.create(matrix_dir, recursive = TRUE, showWarnings = FALSE)
file.create(file.path(matrix_dir, c("barcodes.tsv.gz", "features.tsv.gz", "matrix.mtx.gz")))
#> [1] TRUE TRUE TRUE

TS_collect_cellranger_files(
  input_dir = project,
  dest_dir = file.path(tempdir(), "cellranger_transfer_collect"),
  execute = FALSE
)
#> Proposed Cell Ranger file collection:
#> # A tibble: 3 × 5
#>   sample_id file_group                 source_path              dest_path status
#>   <chr>     <chr>                      <chr>                    <chr>     <chr> 
#> 1 sampleA   filtered_feature_bc_matrix /tmp/RtmpBkuW1o/cellran… /tmp/Rtm… ready 
#> 2 sampleA   filtered_feature_bc_matrix /tmp/RtmpBkuW1o/cellran… /tmp/Rtm… ready 
#> 3 sampleA   filtered_feature_bc_matrix /tmp/RtmpBkuW1o/cellran… /tmp/Rtm… ready 
#> Dry run only. No directories were created and no files were copied.