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Merged
TimothySundell merged 1 commit into from
May 13, 2026
Merged

Now prioritizes all_contig for vdj data #3

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104 changes: 79 additions & 25 deletions R/TS_cellranger_file_collection.R
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,11 @@
#' `cellranger multi` layouts such as `outs/per_sample_outs/<sample>` and for
#' project folders organised as `project/<sample>/cellranger_outs`.
#'
#' The filtered gene expression matrix is detected at sample level. V(D)J
#' directories are detected at run level, for example `outs/vdj_b` and
#' `outs/vdj_t`, because `cellranger multi` stores the unfiltered
#' `all_contig*` files there rather than in `per_sample_outs/<sample>`.
#'
#' @param input_dir Character scalar. Project or Cell Ranger output directory to
#' search.
#' @param sample_regex Optional regular expression used to extract sample names
Expand All @@ -17,8 +22,8 @@
#' @param vdj_dir_names Character vector of V(D)J directory names to detect.
#'
#' @return A tibble with one row per detected sample matrix and columns
#' `sample_id`, `sample_root`, `matrix_dir`, `vdj_b_dir`, `vdj_t_dir`, and
#' `detection_note`.
#' `sample_id`, `sample_root`, `outs_dir`, `matrix_dir`, `vdj_b_dir`,
#' `vdj_t_dir`, and `detection_note`.
#'
#' @examples
#' project <- file.path(tempdir(), "cellranger_project")
Expand Down Expand Up @@ -68,6 +73,7 @@ TS_find_cellranger_samples <- function(
return(tibble::tibble(
sample_id = character(),
sample_root = character(),
outs_dir = character(),
matrix_dir = character(),
vdj_b_dir = character(),
vdj_t_dir = character(),
Expand All @@ -80,14 +86,15 @@ TS_find_cellranger_samples <- function(
matrix_dir,
sample_regex = sample_regex
)
vdj_dirs <- .TS_find_vdj_dirs(
inferred$sample_root,
vdj_dirs <- .TS_find_raw_vdj_dirs(
inferred$outs_dir,
vdj_dir_names = vdj_dir_names
)

tibble::tibble(
sample_id = inferred$sample_id,
sample_root = inferred$sample_root,
outs_dir = inferred$outs_dir,
matrix_dir = matrix_dir,
vdj_b_dir = .TS_first_or_na(vdj_dirs[basename(vdj_dirs) == "vdj_b"]),
vdj_t_dir = .TS_first_or_na(vdj_dirs[basename(vdj_dirs) == "vdj_t"]),
Expand All @@ -102,10 +109,12 @@ TS_find_cellranger_samples <- function(
#'
#' @description
#' Builds a copy plan for selected Cell Ranger files without changing the file
#' system. Matrix files are planned 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 into
#' per-sample `vdj_b` and `vdj_t` directories with the sample name prepended.
#' 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.
#'
#' @param input_dir Character scalar. Project or Cell Ranger output directory to
#' search.
Expand All @@ -115,9 +124,9 @@ TS_find_cellranger_samples <- function(
#' See [TS_find_cellranger_samples()].
#' @param overwrite Logical. If `FALSE`, the function errors when planned target
#' files already exist.
#' @param strict Logical. If `TRUE`, existing V(D)J directories must contain all
#' requested V(D)J files. If `FALSE`, missing V(D)J files are recorded in the
#' plan and available files can still be copied.
#' @param 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.
#' @param ... Additional arguments passed to [TS_find_cellranger_samples()], such
#' as `matrix_dir_names` or `vdj_dir_names`.
#'
Expand Down Expand Up @@ -174,6 +183,8 @@ TS_plan_cellranger_file_collection <- function(
)
}

.TS_validate_cellranger_vdj_sample_scope(samples)

dest_dir <- normalizePath(dest_dir, winslash = "/", mustWork = FALSE)

matrix_files <- c("barcodes.tsv.gz", "features.tsv.gz", "matrix.mtx.gz")
Expand Down Expand Up @@ -273,9 +284,10 @@ TS_plan_cellranger_file_collection <- function(
#'
#' @description
#' Copies selected Cell Ranger files into a transfer-friendly destination
#' directory. Each sample receives its own folder, matrix filenames are kept
#' unchanged for Seurat compatibility, and V(D)J files are renamed with the
#' sample ID as a prefix.
#' 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.
#'
#' @param input_dir Character scalar. Project or Cell Ranger output directory to
#' search.
Expand All @@ -287,9 +299,9 @@ TS_plan_cellranger_file_collection <- function(
#' @param confirm Logical. If `TRUE`, ask for confirmation before copying.
#' @param execute Logical. If `FALSE`, return the planned copy operations without
#' creating directories or copying files.
#' @param strict Logical. If `TRUE`, existing V(D)J directories must contain all
#' requested V(D)J files. If `FALSE`, missing V(D)J files are skipped and
#' recorded in the returned plan.
#' @param 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.
#' @param ... Additional arguments passed to [TS_find_cellranger_samples()], such
#' as `matrix_dir_names` or `vdj_dir_names`.
#'
Expand Down Expand Up @@ -496,6 +508,7 @@ TS_collect_cellranger_files <- function(
sample_index <- marker_index + 1
sample_id <- parts[[sample_index]]
sample_root <- .TS_path_from_parts(parts, sample_index)
outs_dir <- .TS_path_from_parts(parts, marker_index - 1)
detection_note <- paste0(parts[[marker_index]], "/<sample>")
} else {
output_markers <- which(parts %in% c("cellranger_outs", "outs"))
Expand All @@ -505,10 +518,12 @@ TS_collect_cellranger_files <- function(
sample_index <- output_index - 1
sample_id <- parts[[sample_index]]
sample_root <- .TS_path_from_parts(parts, output_index)
outs_dir <- sample_root
detection_note <- paste0(parts[[output_index]], " parent directory")
} else {
sample_id <- basename(dirname(matrix_dir))
sample_root <- dirname(matrix_dir)
outs_dir <- sample_root
detection_note <- "matrix parent directory"
}
}
Expand All @@ -521,22 +536,19 @@ TS_collect_cellranger_files <- function(
list(
sample_id = sample_id,
sample_root = normalizePath(sample_root, winslash = "/", mustWork = TRUE),
outs_dir = normalizePath(outs_dir, winslash = "/", mustWork = TRUE),
detection_note = detection_note
)
}

.TS_find_vdj_dirs <- function(sample_root, vdj_dir_names) {
if (!dir.exists(sample_root)) {
.TS_find_raw_vdj_dirs <- function(outs_dir, vdj_dir_names) {
if (!dir.exists(outs_dir)) {
return(character())
}

direct <- file.path(sample_root, vdj_dir_names)
direct <- file.path(outs_dir, vdj_dir_names)
direct <- direct[dir.exists(direct)]

nested <- .TS_list_dirs(sample_root)
nested <- nested[basename(nested) %in% vdj_dir_names]

unique(normalizePath(c(direct, nested), winslash = "/", mustWork = TRUE))
unique(normalizePath(direct, winslash = "/", mustWork = TRUE))
}

.TS_first_or_na <- function(x) {
Expand All @@ -562,6 +574,48 @@ TS_collect_cellranger_files <- function(
}
}

.TS_validate_cellranger_vdj_sample_scope <- function(samples) {
samples_with_vdj <- dplyr::filter(
samples,
!is.na(.data$vdj_b_dir) | !is.na(.data$vdj_t_dir)
)

if (nrow(samples_with_vdj) == 0) {
return(invisible(samples))
}

outs_counts <- dplyr::summarise(
dplyr::group_by(samples_with_vdj, .data$outs_dir),
n = dplyr::n_distinct(.data$sample_id),
.groups = "drop"
)
multi_sample_outs <- dplyr::filter(outs_counts, .data$n > 1)

if (nrow(multi_sample_outs) == 0) {
return(invisible(samples))
}

affected_samples <- dplyr::filter(
samples_with_vdj,
.data$outs_dir %in% multi_sample_outs$outs_dir
)

stop(
"Raw V(D)J all_contig files are run-level outputs, not sample-level outputs. ",
"Multiple samples were detected under the same outs directory, so these ",
"raw V(D)J files will not be copied into per-sample folders automatically:\n",
paste(
paste0(
affected_samples$outs_dir,
" -> ",
affected_samples$sample_id
),
collapse = "\n"
),
call. = FALSE
)
}

.TS_plan_one_cellranger_sample <- function(
sample_row,
dest_dir,
Expand Down
14 changes: 8 additions & 6 deletions man/TS_collect_cellranger_files.Rd
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14 changes: 10 additions & 4 deletions man/TS_find_cellranger_samples.Rd
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17 changes: 10 additions & 7 deletions man/TS_plan_cellranger_file_collection.Rd
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