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Plan collection of selected Cell Ranger files

TS_plan_cellranger_file_collection.Rd

Builds a copy plan for selected Cell Ranger files without changing the file system. Matrix files are planned from sample-level filtered matrix output into per-sample filtered_feature_bc_matrix directories with their original filenames, so they remain directly readable by Seurat. V(D)J files are planned from run-level unfiltered outs/vdj_b and outs/vdj_t directories into per-sample vdj_b and vdj_t directories with the sample name prepended.

Usage

TS_plan_cellranger_file_collection(
  input_dir,
  dest_dir,
  sample_regex = NULL,
  overwrite = FALSE,
  strict = TRUE,
  ...
)

Arguments

input_dir

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

dest_dir

Character scalar. Destination directory for the collected sample folders.

sample_regex

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

overwrite

Logical. If FALSE, the function errors when planned target files already exist.

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 recorded in the plan and available files can still be copied.

...

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

Value

A tibble with one row per planned or missing file. Important columns include sample_id, file_group, source_path, dest_path, source_exists, copy, and status.

Examples

project <- file.path(tempdir(), "cellranger_project_plan")
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

plan <- TS_plan_cellranger_file_collection(
  input_dir = project,
  dest_dir = file.path(tempdir(), "cellranger_transfer_plan")
)
plan
#> # A tibble: 3 × 12
#>   sample_id file_group           source_dir source_filename source_path dest_dir
#>   <chr>     <chr>                <chr>      <chr>           <chr>       <chr>   
#> 1 sampleA   filtered_feature_bc… /tmp/Rtmp… barcodes.tsv.gz /tmp/RtmpB… /tmp/Rt…
#> 2 sampleA   filtered_feature_bc… /tmp/Rtmp… features.tsv.gz /tmp/RtmpB… /tmp/Rt…
#> 3 sampleA   filtered_feature_bc… /tmp/Rtmp… matrix.mtx.gz   /tmp/RtmpB… /tmp/Rt…
#> # ℹ 6 more variables: dest_filename <chr>, dest_path <chr>, required <lgl>,
#> #   source_exists <lgl>, copy <lgl>, status <chr>