diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..9853ba3
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,127 @@
+name: tests
+
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      run_conda_validation:
+        description: "Create workflow conda envs and run package import checks"
+        required: false
+        default: false
+        type: boolean
+      run_container_validation:
+        description: "Pull workflow containers"
+        required: false
+        default: false
+        type: boolean
+      run_doubletfinder_install:
+        description: "Run the networked DoubletFinder GitHub install rule"
+        required: false
+        default: false
+        type: boolean
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      SNAKEMAKE_CONDA_FRONTEND: mamba
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Create test environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Cache Snakemake rule environments
+        uses: actions/cache@v4
+        with:
+          path: .snakemake/conda
+          key: snakemake-conda-${{ runner.os }}-${{ hashFiles('workflow/envs/*.yml') }}
+          restore-keys: |
+            snakemake-conda-${{ runner.os }}-
+
+      - name: Run tests
+        run: pytest tests -q
+
+  conda-validation:
+    if: github.event_name == 'workflow_dispatch' && inputs.run_conda_validation
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        env_name:
+          - cellbender.yml
+          - doubletfinder.yml
+          - emptydrops.yml
+          - posthocfilter.yml
+          - scdblfinder.yml
+          - soupx.yml
+          - tenx2seuratrds.yml
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      SNAKEMAKE_CONDA_FRONTEND: mamba
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Create test environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Run conda validation for ${{ matrix.env_name }}
+        run: pytest tests/test_conda_container_validation.py --run-conda-validation --conda-env-name "${{ matrix.env_name }}" -q
+
+  container-validation:
+    if: github.event_name == 'workflow_dispatch' && inputs.run_container_validation
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Create test environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Run container validation
+        run: pytest tests/test_conda_container_validation.py --run-container-validation -q
+
+  doubletfinder-install:
+    if: github.event_name == 'workflow_dispatch' && inputs.run_doubletfinder_install
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      SNAKEMAKE_CONDA_FRONTEND: mamba
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Create test environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Run DoubletFinder install validation
+        run: pytest tests/test_conda_container_validation.py --run-doubletfinder-install -q
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..cb76481
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,21 @@
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.cache/
+Rplots.pdf
+logs/
+.snakemake/
+.jupyter/
+.vscode/
+.ipython/
+scratch/
+*err
+*out
+results/
+testdata/results/
+# Keep golden test outputs trackable even though results/ is ignored.
+!tests/reference_outputs/
+!tests/reference_outputs/**
+!tests/reference_outputs/testdata/
+!tests/reference_outputs/testdata/results/
+!tests/reference_outputs/testdata/results/**
diff --git a/config/config.yaml b/config/config.yaml
index 9f649ed..6ac8b47 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,6 +1,7 @@
 conda-channel-priority: "strict"
 
 sampleTable: "samplesheet.tsv"
+workflow_seed: 12345
 
 emptydrop_removal_methods: ["tenx","emptydrops"]
 ambient_decon_methods: ["soupx","cellbender_fromraw"]
diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..67be718
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,13 @@
+name: scrnaseq-preprocessing-tests
+channels:
+  - conda-forge
+  - bioconda
+channel_priority: strict
+dependencies:
+  - python=3.12
+  - pytest
+  - pyyaml
+  - snakemake=9.16.3
+  - conda
+  - mamba
+  - hdf5
diff --git a/testdata/filtered_feature_bc_matrix/barcodes.tsv.gz b/testdata/filtered_feature_bc_matrix/barcodes.tsv.gz
new file mode 100644
index 0000000..caff0a3
Binary files /dev/null and b/testdata/filtered_feature_bc_matrix/barcodes.tsv.gz differ
diff --git a/testdata/filtered_feature_bc_matrix/features.tsv.gz b/testdata/filtered_feature_bc_matrix/features.tsv.gz
new file mode 100644
index 0000000..b4ba99b
Binary files /dev/null and b/testdata/filtered_feature_bc_matrix/features.tsv.gz differ
diff --git a/testdata/filtered_feature_bc_matrix/matrix.mtx.gz b/testdata/filtered_feature_bc_matrix/matrix.mtx.gz
new file mode 100644
index 0000000..10c2d9d
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diff --git a/testdata/raw_feature_bc_matrix.h5 b/testdata/raw_feature_bc_matrix.h5
new file mode 100644
index 0000000..98a30e1
Binary files /dev/null and b/testdata/raw_feature_bc_matrix.h5 differ
diff --git a/testdata/raw_feature_bc_matrix/barcodes.tsv.gz b/testdata/raw_feature_bc_matrix/barcodes.tsv.gz
new file mode 100644
index 0000000..b428a33
Binary files /dev/null and b/testdata/raw_feature_bc_matrix/barcodes.tsv.gz differ
diff --git a/testdata/raw_feature_bc_matrix/features.tsv.gz b/testdata/raw_feature_bc_matrix/features.tsv.gz
new file mode 100644
index 0000000..b4ba99b
Binary files /dev/null and b/testdata/raw_feature_bc_matrix/features.tsv.gz differ
diff --git a/testdata/raw_feature_bc_matrix/matrix.mtx.gz b/testdata/raw_feature_bc_matrix/matrix.mtx.gz
new file mode 100644
index 0000000..b2fb32f
Binary files /dev/null and b/testdata/raw_feature_bc_matrix/matrix.mtx.gz differ
diff --git a/testdata/samplesheet_test.tsv b/testdata/samplesheet_test.tsv
new file mode 100644
index 0000000..b36d643
--- /dev/null
+++ b/testdata/samplesheet_test.tsv
@@ -0,0 +1,2 @@
+sampleid	tenx_datadir
+test	testdata
diff --git a/tests/README.md b/tests/README.md
new file mode 100644
index 0000000..bffdefe
--- /dev/null
+++ b/tests/README.md
@@ -0,0 +1,64 @@
+# Tests
+
+These tests are intended to run from the repository root in any environment where `snakemake` and `pytest` are available on `PATH`. How that environment is created or activated is site-specific; for example, an HPC may require loading a module before `conda activate` is available.
+
+Example:
+
+```bash
+conda env create -f environment.yml
+conda activate scrnaseq-preprocessing-tests
+pytest tests
+```
+
+`python -m pytest tests` is also fine when `python` resolves to the same environment that provides `pytest` and `snakemake`. If it does not, the active shell is likely resolving commands from different environments. Confirm with:
+
+```bash
+which python
+which pytest
+which snakemake
+```
+
+The dry-run DAG test uses the small CellRanger-style input data in `testdata/` and the test-specific sample sheet `testdata/samplesheet_test.tsv`. The tests override `sampleTable` on the Snakemake command line, so they do not use the normal workflow `samplesheet.tsv`. They do not require `--conda-prefix`, a cluster profile, or any site-specific paths. Sample-sheet validation tests cover malformed headers, duplicate sample IDs, missing or incomplete 10x data paths, absolute `tenx_datadir` values, and multi-sample DAG expansion. Config validation tests cover required keys, allowed method values, threshold types/ranges, invalid-config failures, and dry-run DAG variants driven by method-list config changes. The default suite also runs `snakemake --lint` against the test-data configuration, which catches workflow-structure problems such as missing `log:` directives, helper functions embedded in rule files, long `run:` blocks that should live in scripts, path-composition warnings, missing rule-level conda/container declarations, and shell commands that directly interpolate global workflow variables instead of passing values through `params`.
+
+GitHub Actions runs the default test suite via `.github/workflows/tests.yml`, using the same top-level `environment.yml` test runner environment and caching Snakemake-created rule environments under `.snakemake/conda`.
+
+The default test suite also includes a focused local rule-execution smoke test. It runs the real `tenx2seuratrds`, `find_markers`, and `combine_markers` rule chain against `testdata/`, using Snakemake's `--use-conda` support and writing outputs under pytest's temporary directory. This catches broken R package imports, script argument drift, invalid Seurat object creation, and marker CSV schema changes without submitting to SLURM.
+
+The R output validator also checks that the Seurat object has at least 100 features and 100 cells; metadata rows match the cell count; barcode row names are present, unique, and nonempty; `orig.ident`, `nCount_RNA`, `nFeature_RNA`, `percent.mt`, and `seurat_clusters` metadata columns exist; RNA count and feature-count metadata values are finite and positive; mitochondrial percentages are finite and within `[0, 100]`; at least two clusters are present; PCA and UMAP reductions exist; the marker table is nonempty and has the expected columns; marker gene symbols are present and nonempty; marker numeric columns are finite; marker p-value and percent columns are within `[0, 1]`; marker clusters are present in the Seurat metadata; markers are reported for at least two clusters; and the marker `workflow` column matches the expected test workflow label. The test runner environment is defined in the repository-level `environment.yml`; the rule-specific R environment is still created by Snakemake from `workflow/envs/tenx2seuratrds.yml`. A separate lightweight checkpoint-expansion test uses a fake `Rscript` to materialize the `marker_manifest` checkpoint, verify that dynamic `find_markers` jobs are generated for each cluster id, and confirm that `combine_markers` receives the expected marker chunks.
+
+
+## Optional conda and container validation
+
+The default suite validates that workflow conda environment files are well formed, that rule-level conda references resolve to existing files, and that container declarations are recognizable. Expensive network-dependent validation is opt-in:
+
+```bash
+pytest tests --run-conda-validation
+pytest tests --run-container-validation
+pytest tests --run-doubletfinder-install
+```
+
+`--run-conda-validation` creates each `workflow/envs/*.yml` environment in a pytest temporary directory and checks key R/Python package imports. To validate only one environment, pass `--conda-env-name ENV_FILE`, for example `--conda-env-name soupx.yml`; GitHub Actions uses this selector to run conda validation as one matrix job per env. `--run-container-validation` pulls the CellBender container with Docker, Apptainer, or Singularity. `--run-doubletfinder-install` runs the networked Snakemake `install_doubletfinder` rule and confirms that `DoubletFinder` can be imported from the created rule environment.
+
+
+## Optional full workflow run
+
+The default tests build and inspect the DAG and run a focused local R-rule smoke test. To submit the full test-data workflow and verify all declared outputs against the reference snapshot, opt in explicitly:
+
+```bash
+pytest tests --run-workflow
+```
+
+The full-run test calls `tests/run_test_workflow.sh`, which uses `testdata/samplesheet_test.tsv` and overrides the workflow output directory with `resultsDir=testdata/results`. The manifest in `tests/test_sample_rule_output_files.txt` is therefore written with paths under `testdata/results/`.
+
+For testing, omit `--snakemake-conda-prefix` so Snakemake uses its default `.snakemake/conda` location under the repository root. The runner assumes that the current environment already provides `snakemake` on `PATH`.
+
+
+## Reference outputs
+
+The full workflow test compares regenerated files in `testdata/results/` against reference files under `tests/reference_outputs/`. The compared file list is in `tests/test_reference_output_files.txt`. Seurat `.rds` files are compared at the metadata-table level, marker CSVs are compared by columns and `(cluster, genesymbol)` rows with numeric tolerance, emptyDrops matrix files are compared after gzip decompression, CellBender H5 outputs are compared with `h5diff`, and remaining durable outputs are compared byte-for-byte.
+
+To refresh the reference snapshot after intentionally changing workflow behavior, first run the full test workflow so `testdata/results/` contains the desired outputs, then run:
+
+```bash
+python tests/update_reference_outputs.py
+```
diff --git a/tests/compare_seurat_metadata.R b/tests/compare_seurat_metadata.R
new file mode 100644
index 0000000..6a2e638
--- /dev/null
+++ b/tests/compare_seurat_metadata.R
@@ -0,0 +1,97 @@
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 0 || length(args) %% 2 != 0) {
+  stop("Provide current/reference RDS path pairs", call. = FALSE)
+}
+
+suppressPackageStartupMessages(library("Seurat"))
+
+numeric_tolerance <- as.numeric(Sys.getenv("SEURAT_METADATA_NUMERIC_TOLERANCE", "1e-8"))
+if (is.na(numeric_tolerance) || length(numeric_tolerance) != 1) {
+  stop("SEURAT_METADATA_NUMERIC_TOLERANCE must be numeric", call. = FALSE)
+}
+
+fail <- function(path, message) {
+  stop(sprintf("%s: %s", path, message), call. = FALSE)
+}
+
+compare_metadata_column <- function(current_path, column, current_values, reference_values) {
+  current_na <- is.na(current_values)
+  reference_na <- is.na(reference_values)
+  if (!identical(current_na, reference_na)) {
+    fail(current_path, sprintf("metadata column %s has different NA positions", column))
+  }
+
+  both_numeric <- is.numeric(current_values) && is.numeric(reference_values)
+  both_integer <- is.integer(current_values) && is.integer(reference_values)
+  if (both_numeric || both_integer) {
+    current_numeric <- as.numeric(current_values)
+    reference_numeric <- as.numeric(reference_values)
+    comparable <- !current_na & !reference_na
+    if (any(comparable)) {
+      diff <- abs(current_numeric[comparable] - reference_numeric[comparable])
+      scale <- pmax(abs(current_numeric[comparable]), abs(reference_numeric[comparable]), 1)
+      bad <- diff > numeric_tolerance * scale
+      if (any(bad)) {
+        fail(
+          current_path,
+          sprintf(
+            "metadata column %s differs numerically; max abs diff %.12g",
+            column,
+            max(diff)
+          )
+        )
+      }
+    }
+    return(invisible(TRUE))
+  }
+
+  current_character <- as.character(current_values)
+  reference_character <- as.character(reference_values)
+  comparable <- !current_na & !reference_na
+  if (!identical(current_character[comparable], reference_character[comparable])) {
+    fail(current_path, sprintf("metadata column %s differs", column))
+  }
+
+  invisible(TRUE)
+}
+
+compare_metadata_pair <- function(current_path, reference_path) {
+  current <- readRDS(current_path)
+  reference <- readRDS(reference_path)
+
+  current_metadata <- current@meta.data
+  reference_metadata <- reference@meta.data
+
+  if (!identical(colnames(current_metadata), colnames(reference_metadata))) {
+    fail(
+      current_path,
+      paste0(
+        "metadata columns differ\ncurrent: ",
+        paste(colnames(current_metadata), collapse = ","),
+        "\nreference: ",
+        paste(colnames(reference_metadata), collapse = ",")
+      )
+    )
+  }
+
+  if (!identical(rownames(current_metadata), rownames(reference_metadata))) {
+    fail(current_path, "metadata barcodes differ")
+  }
+
+  for (column in colnames(current_metadata)) {
+    compare_metadata_column(
+      current_path,
+      column,
+      current_metadata[[column]],
+      reference_metadata[[column]]
+    )
+  }
+
+  invisible(TRUE)
+}
+
+for (i in seq(1, length(args), by = 2)) {
+  compare_metadata_pair(args[[i]], args[[i + 1]])
+}
+
+cat(sprintf("Compared Seurat metadata for %d object(s)\n", length(args) / 2))
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..4e69f78
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,36 @@
+def pytest_addoption(parser):
+    parser.addoption(
+        "--run-workflow",
+        action="store_true",
+        default=False,
+        help="run the full Snakemake workflow on the test data",
+    )
+    parser.addoption(
+        "--snakemake-conda-prefix",
+        default=None,
+        help="optional value to pass to Snakemake --conda-prefix for --run-workflow",
+    )
+    parser.addoption(
+        "--run-conda-validation",
+        action="store_true",
+        default=False,
+        help="create workflow conda environments and validate key package imports",
+    )
+    parser.addoption(
+        "--conda-env-name",
+        default=None,
+        help="optional workflow/envs/*.yml filename to validate with --run-conda-validation",
+    )
+    parser.addoption(
+        "--run-container-validation",
+        action="store_true",
+        default=False,
+        help="pull workflow containers with docker, apptainer, or singularity",
+    )
+    parser.addoption(
+        "--run-doubletfinder-install",
+        action="store_true",
+        default=False,
+        help="execute the DoubletFinder GitHub install rule on test outputs",
+    )
+
diff --git a/tests/reference_outputs/testdata/results/cellbender/cellbender_test.h5 b/tests/reference_outputs/testdata/results/cellbender/cellbender_test.h5
new file mode 100644
index 0000000..b8d668b
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diff --git a/tests/reference_outputs/testdata/results/cellbender/cellbender_test_filtered.h5 b/tests/reference_outputs/testdata/results/cellbender/cellbender_test_filtered.h5
new file mode 100644
index 0000000..9be81a1
Binary files /dev/null and b/tests/reference_outputs/testdata/results/cellbender/cellbender_test_filtered.h5 differ
diff --git a/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..36e4d3d
Binary files /dev/null and b/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..89d2ea5
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test_markergenes.csv
@@ -0,0 +1,203 @@
+genesymbol,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,workflow
+Myt1l,3.971037213949109e-28,-3.854800385471793,0.357,0.991,3.260221552652219e-25,3,seurat_cellbender_fromraw_test
+Slco1c1,9.359392871918687e-21,4.185000321904411,0.518,0.041,7.684061547845243e-18,3,seurat_cellbender_fromraw_test
+Rdm1,3.6952356820901395e-19,4.510622900349515,0.446,0.027,3.033788494996005e-16,3,seurat_cellbender_fromraw_test
+Nde1,1.4117230537785938e-18,4.288230479013067,0.5,0.05,1.1590246271522255e-15,3,seurat_cellbender_fromraw_test
+Rpl13,8.169656110146415e-17,0.6968685377415946,1,1,6.707287666430206e-14,3,seurat_cellbender_fromraw_test
+Ube2c,9.084497648085416e-17,4.633223601450396,0.5,0.063,7.458372569078126e-14,3,seurat_cellbender_fromraw_test
+Pax6,1.988234112902989e-16,3.36320943017775,0.589,0.108,1.632340206693354e-13,3,seurat_cellbender_fromraw_test
+Phactr1,2.544137425423247e-16,-1.8328065890786511,0.661,0.977,2.0887368262724858e-13,3,seurat_cellbender_fromraw_test
+Elk3,3.8333141039569214e-16,4.605970776936996,0.375,0.023,3.147150879348633e-13,3,seurat_cellbender_fromraw_test
+Mt2,7.028657576842482e-15,4.410272375017046,0.339,0.018,5.770527870587677e-12,3,seurat_cellbender_fromraw_test
+Cenpn,1.0955904865543372e-14,3.630917134067227,0.304,0.009,8.994797894611107e-12,3,seurat_cellbender_fromraw_test
+Hes1,4.1470348309045864e-14,6.344612948910585,0.268,0.005,3.404715596172665e-11,3,seurat_cellbender_fromraw_test
+Tpbg,5.1301495376227256e-14,4.308989039179864,0.321,0.018,4.211852770388258e-11,3,seurat_cellbender_fromraw_test
+Psrc1,3.0378339354322593e-13,3.656912342600171,0.339,0.027,2.494061660989885e-10,3,seurat_cellbender_fromraw_test
+Rpsa,6.839876351879871e-13,0.816372294657667,1,1,5.615538484893374e-10,3,seurat_cellbender_fromraw_test
+Rpl26,1.1743579168722405e-12,0.6203629792851166,1,1,9.641478497521092e-10,3,seurat_cellbender_fromraw_test
+Fnbp1l,1.3994032502777844e-12,-1.2769323815107192,0.679,0.982,1.1489100684780607e-9,3,seurat_cellbender_fromraw_test
+Serf2,2.651157609323483e-12,0.84799690655495,0.982,0.973,2.176600397254579e-9,3,seurat_cellbender_fromraw_test
+Plxna4,5.591901420177461e-12,-2.515872312981382,0.411,0.842,4.5909510659656956e-9,3,seurat_cellbender_fromraw_test
+Ccnd1,8.424171905594535e-12,4.124564468042436,0.321,0.032,6.916245134493114e-9,3,seurat_cellbender_fromraw_test
+Gypc,1.781563750672596e-11,5.687500662433594,0.196,0,1.4626638393022012e-8,3,seurat_cellbender_fromraw_test
+Hivep3,1.7854461440388307e-11,-2.4364051770569226,0.25,0.739,1.4658512842558801e-8,3,seurat_cellbender_fromraw_test
+Sept9,4.041061619236838e-11,1.987060944292502,0.625,0.198,3.3177115893934445e-8,3,seurat_cellbender_fromraw_test
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diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..58f92ed
Binary files /dev/null and b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..47dc395
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..9ae38dd
Binary files /dev/null and b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..b034713
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test.rds
new file mode 100644
index 0000000..3c544de
Binary files /dev/null and b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..21eedbc
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,144 @@
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diff --git a/tests/reference_outputs/testdata/results/doubletfinder_installed.txt b/tests/reference_outputs/testdata/results/doubletfinder_installed.txt
new file mode 100644
index 0000000..e69de29
diff --git a/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test.rds b/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test.rds
new file mode 100644
index 0000000..8ab1f56
Binary files /dev/null and b/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..6b3cdcb
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/emptydrops/filtered_seurat_emptydrops_test_markergenes.csv
@@ -0,0 +1,195 @@
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diff --git a/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/barcodes.tsv.gz b/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/barcodes.tsv.gz
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diff --git a/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/features.tsv.gz b/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/features.tsv.gz
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diff --git a/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/matrix.mtx.gz b/tests/reference_outputs/testdata/results/emptydrops/test_emptydrops_filtered_matrix/matrix.mtx.gz
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test.rds
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..02dabbc
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test_markergenes.csv
@@ -0,0 +1,108 @@
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..ddb1bf3
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..1b4e55a
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test.rds
new file mode 100644
index 0000000..9284b91
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..f8654cd
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,144 @@
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..7486012
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..f11d712
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..7dc21f8
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..a16e5bc
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test.rds
new file mode 100644
index 0000000..7e29924
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..df4e957
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,121 @@
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..897ac44
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..eccbbe7
--- /dev/null
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..154d9be
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test_markergenes.csv
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index 0000000..5c888da
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..ef53957
--- /dev/null
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..aa3a9a4
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..f87e798
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..5d65ea0
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..d30496d
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test_markergenes.csv
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diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test.rds
new file mode 100644
index 0000000..5bb0c74
Binary files /dev/null and b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..dcfe477
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,129 @@
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diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test.rds b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test.rds
new file mode 100644
index 0000000..93113aa
Binary files /dev/null and b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv
new file mode 100644
index 0000000..e2c4d90
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv
@@ -0,0 +1,194 @@
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diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..a12609f
Binary files /dev/null and b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..d0ad1e1
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test_markergenes.csv
@@ -0,0 +1,182 @@
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diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test.rds
new file mode 100644
index 0000000..56d02c4
Binary files /dev/null and b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..102c567
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,121 @@
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diff --git a/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test.rds b/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test.rds
new file mode 100644
index 0000000..b7224f7
Binary files /dev/null and b/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test_markergenes.csv
new file mode 100644
index 0000000..1f15457
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/seurat_filtered/filtered_seurat_tenx_test_markergenes.csv
@@ -0,0 +1,139 @@
+genesymbol,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,workflow
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diff --git a/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test.rds b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test.rds
new file mode 100644
index 0000000..d3403c0
Binary files /dev/null and b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test_markergenes.csv b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test_markergenes.csv
new file mode 100644
index 0000000..8574663
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_emptydrops_test_markergenes.csv
@@ -0,0 +1,188 @@
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diff --git a/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test.rds b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test.rds
new file mode 100644
index 0000000..848d99e
Binary files /dev/null and b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test.rds differ
diff --git a/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test_markergenes.csv b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test_markergenes.csv
new file mode 100644
index 0000000..b8a2161
--- /dev/null
+++ b/tests/reference_outputs/testdata/results/soupx/seurat_soupx_tenx_test_markergenes.csv
@@ -0,0 +1,120 @@
+genesymbol,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,workflow
+Myt1l,1.5315737400102693e-22,1.3661552350656705,1,0.749,1.2482325981083694e-19,1,seurat_soupx_tenx_test
+Rpl13,5.437488290235946e-18,-0.7331396074786389,0.992,1,4.431552956542296e-15,1,seurat_soupx_tenx_test
+Mef2c,1.0666041033005368e-16,1.790227469859231,0.843,0.436,8.692823441899374e-14,1,seurat_soupx_tenx_test
+Rpsa,4.6209081400543706e-15,-0.92916245266166,0.992,0.989,3.766040134144312e-12,1,seurat_soupx_tenx_test
+Phactr1,1.3582130974787177e-13,0.9382505309138248,1,0.832,1.1069436744451549e-10,1,seurat_soupx_tenx_test
+Cep170,2.738767687809232e-13,1.1761465822839978,0.86,0.637,2.2320956655645238e-10,1,seurat_soupx_tenx_test
+Fau,6.550340951921384e-13,-0.6086301982791742,0.975,1,5.338527875815927e-10,1,seurat_soupx_tenx_test
+Rpl26,6.1686367685406666e-12,-0.6402837772481331,1,0.989,5.027438966360643e-9,1,seurat_soupx_tenx_test
+Plxna4,1.54724398510984e-11,1.3906956180893817,0.843,0.631,1.2610038478645197e-8,1,seurat_soupx_tenx_test
+Hnrnpa1,3.2556908713433404e-11,-0.7366164672631217,0.983,0.983,2.6533880601448224e-8,1,seurat_soupx_tenx_test
+Rpl19,1.8921595095489582e-10,-0.5655711118402809,1,1,1.542110000282401e-7,1,seurat_soupx_tenx_test
+Insm1,8.979164678541713e-10,-1.7746775566311594,0.355,0.682,7.318019213011497e-7,1,seurat_soupx_tenx_test
+Mmd2,9.644500042318756e-10,-1.894479078647635,0.207,0.547,7.860267534489786e-7,1,seurat_soupx_tenx_test
+Fnbp1l,1.0857728063810364e-9,0.7543809052485149,0.983,0.827,8.849048372005449e-7,1,seurat_soupx_tenx_test
+Abr,1.356985887456183e-9,1.4816970363403097,0.669,0.458,1.1059434982767893e-6,1,seurat_soupx_tenx_test
+Snhg14,1.3892161552213347e-9,1.3392397603616026,0.719,0.436,1.1322111665053875e-6,1,seurat_soupx_tenx_test
+Hivep3,1.6877025204145204e-9,1.299015326253231,0.785,0.525,1.3754775541378344e-6,1,seurat_soupx_tenx_test
+Hsp90ab1,1.751449389415208e-9,-0.5469266684216594,1,1,1.4274312523733943e-6,1,seurat_soupx_tenx_test
+Psmc2,1.1840806065770258e-8,-1.1369661070773431,0.463,0.737,9.65025694360276e-6,1,seurat_soupx_tenx_test
+Pax6,1.2209772476030218e-8,-4.341938055618856,0.025,0.279,9.950964567964627e-6,1,seurat_soupx_tenx_test
+Dpysl2,3.948108124003597e-8,0.6270382412382236,0.967,0.922,3.217708121062932e-5,1,seurat_soupx_tenx_test
+Rian,4.6332137655224866e-8,1.6034266878042978,0.438,0.151,3.776069218900826e-5,1,seurat_soupx_tenx_test
+Clic4,9.957119661912585e-8,-1.6166542665002857,0.231,0.536,8.115052524458756e-5,1,seurat_soupx_tenx_test
+Adamts2,1.2248958635885084e-7,2.2936505181722677,0.306,0.078,9.982901288246342e-5,1,seurat_soupx_tenx_test
+Serf2,1.4680738387027218e-7,-0.7083236935940165,0.942,0.972,1.1964801785427184e-4,1,seurat_soupx_tenx_test
+Rplp2,3.794557085812499e-7,-0.5016721918978058,0.975,1,3.092564024937187e-4,1,seurat_soupx_tenx_test
+Slco1c1,3.971887407881893e-7,-5.989636311687976,0,0.19,3.2370882374237425e-4,1,seurat_soupx_tenx_test
+Eef1g,4.896273417286543e-7,-0.5797524714633735,0.86,0.972,3.990462835088533e-4,1,seurat_soupx_tenx_test
+Ube2c,5.973644952128708e-7,-6.989636311687976,0.008,0.201,4.8685206359848967e-4,1,seurat_soupx_tenx_test
+Pdzd11,6.202103584637284e-7,-1.1850692070019906,0.231,0.531,5.054714421479387e-4,1,seurat_soupx_tenx_test
+Jakmip2,8.344563919831991e-7,1.0252192932615034,0.719,0.553,6.800819594663073e-4,1,seurat_soupx_tenx_test
+Tmem50a,1.0975761102313182e-6,-0.8794595614226954,0.446,0.726,8.945245298385243e-4,1,seurat_soupx_tenx_test
+Atp5a1,1.1521227887728843e-6,-0.53767407216381,0.893,0.989,9.389800728499008e-4,1,seurat_soupx_tenx_test
+Nde1,1.53258534276143e-6,-4.624872018890356,0.008,0.19,0.00124905705435056,1,seurat_soupx_tenx_test
+Gps1,2.290300600558177e-6,-0.8155572761609107,0.521,0.788,0.00186659498945491,1,seurat_soupx_tenx_test
+Rpl17,5.721577507370033e-6,-0.45934037331228206,0.959,0.994,0.00466308566850657,1,seurat_soupx_tenx_test
+Iqsec3,8.345174231463598e-6,2.3950275385473496,0.198,0.039,0.00680131699864283,1,seurat_soupx_tenx_test
+Gprc5b,1.2657408317114928e-5,-2.5505246774302743,0.041,0.223,0.01031578777844866,1,seurat_soupx_tenx_test
+Prkar2b,2.4565093919727697e-5,1.193858388298415,0.587,0.385,0.02002055154457807,1,seurat_soupx_tenx_test
+Rpl5,3.4186665424622475e-5,-0.5122904589427983,0.876,0.927,0.02786213232106731,1,seurat_soupx_tenx_test
+Ankrd37,4.2602891757003984e-5,-4.29302845513791,0,0.128,0.03472135678195825,1,seurat_soupx_tenx_test
+Gm42851,4.590984894289811e-5,2.680429757409598,0.157,0.028,0.03741652688846195,1,seurat_soupx_tenx_test
+Rpn2,4.599536236591677e-5,-0.9244323007492632,0.289,0.542,0.03748622032822216,1,seurat_soupx_tenx_test
+Atp5mpl,5.41328065085141e-5,-0.5649777640554718,0.744,0.922,0.04411823730443899,1,seurat_soupx_tenx_test
+Slco1c1,7.33031810617757e-24,4.443664302778981,0.929,0.073,5.9742092565347206e-21,2,seurat_soupx_tenx_test
+Baalc,9.275639552832414e-22,5.439979255971124,0.571,0.021,7.559646235558416e-19,2,seurat_soupx_tenx_test
+Hes1,2.9625311860963907e-18,3.0305883198334227,0.571,0.028,2.414462916668559e-15,2,seurat_soupx_tenx_test
+Mt2,3.7297815394679716e-17,4.081214392903391,0.643,0.045,3.0397719546663974e-14,2,seurat_soupx_tenx_test
+Eepd1,1.777383104665822e-15,4.0570605311946135,0.714,0.073,1.448567230302645e-12,2,seurat_soupx_tenx_test
+Tcf7l1,1.3197797351308588e-14,3.8379432418910273,0.571,0.042,1.07562048413165e-11,2,seurat_soupx_tenx_test
+Elk3,1.360276914476992e-14,3.767553913999629,0.643,0.059,1.1086256852987484e-11,2,seurat_soupx_tenx_test
+Dync2li1,3.0780172893314246e-14,3.3525164147207853,0.857,0.126,2.5085840908051108e-11,2,seurat_soupx_tenx_test
+Nde1,6.481122921231778e-13,3.686935453791345,0.714,0.087,5.282115180803899e-10,2,seurat_soupx_tenx_test
+Idi1,2.159679005935013e-12,4.01266641183616,0.857,0.192,1.760138389837035e-9,2,seurat_soupx_tenx_test
+Cth,2.7138797690885316e-11,4.937478915441941,0.286,0.01,2.2118120118071537e-8,2,seurat_soupx_tenx_test
+Rdm1,1.1186509775244451e-10,4.121190868614329,0.571,0.073,9.117005466824229e-8,2,seurat_soupx_tenx_test
+Pax6,1.1254512261295304e-10,2.9714262473652795,0.786,0.147,9.172427492955673e-8,2,seurat_soupx_tenx_test
+Anxa5,1.9283903231160606e-10,3.1825914132784727,0.5,0.049,1.5716381133395898e-7,2,seurat_soupx_tenx_test
+Ptgfrn,4.5509378075498156e-10,3.164889411545014,0.643,0.098,3.7090143131531e-7,2,seurat_soupx_tenx_test
+Rhcg,3.671292058708454e-9,4.937478915441941,0.214,0.007,2.9921030278473906e-6,2,seurat_soupx_tenx_test
+Plcd4,7.360875153970088e-9,4.767553913999629,0.286,0.017,5.999113250485622e-6,2,seurat_soupx_tenx_test
+Rgma,2.2929138743151732e-8,2.1045889012771997,0.857,0.203,1.8687248075668663e-5,2,seurat_soupx_tenx_test
+Fnbp1l,2.4861611239538373e-8,-3.5498586997652404,0.214,0.923,2.0262213160223773e-5,2,seurat_soupx_tenx_test
+Myt1l,2.9156656215145327e-8,-5.978400463393832,0.071,0.888,2.376267481534344e-5,2,seurat_soupx_tenx_test
+Fras1,4.9961712236463655e-8,3.574908836057233,0.429,0.052,4.071879547271788e-5,2,seurat_soupx_tenx_test
+Polr3h,7.301949695574973e-8,2.449192434132459,0.857,0.266,5.9510890018936024e-5,2,seurat_soupx_tenx_test
+Srebf1,9.262101277486649e-8,2.883031131419565,0.571,0.098,7.548612541151618e-5,2,seurat_soupx_tenx_test
+Ostm1,1.068028459112306e-7,2.565920052829979,0.714,0.175,8.704431941765293e-5,2,seurat_soupx_tenx_test
+Gdi2,1.2047655027438678e-7,1.4833030222561394,1,0.78,9.818838847362522e-5,2,seurat_soupx_tenx_test
+Tpbg,2.671307532258456e-7,2.700439718141092,0.429,0.056,2.1771156387906417e-4,2,seurat_soupx_tenx_test
+Ephb3,4.533062109331496e-7,3.3525164147207853,0.286,0.024,3.6944456191051695e-4,2,seurat_soupx_tenx_test
+Gypc,4.533062109331496e-7,3.504519508165835,0.286,0.024,3.6944456191051695e-4,2,seurat_soupx_tenx_test
+Phactr1,4.578548320191324e-7,-3.0018331578589543,0.357,0.927,3.7315168809559293e-4,2,seurat_soupx_tenx_test
+C030005K06Rik,1.0542877151617604e-6,5.61555082055458,0.214,0.014,8.592444878568348e-4,2,seurat_soupx_tenx_test
+Marc2,1.4035359130435904e-6,1.810622635891515,0.857,0.241,0.00114388176913052,2,seurat_soupx_tenx_test
+Calm2,1.7532761273832885e-6,-1.70768821948513,0.786,0.99,0.00142892004381737,2,seurat_soupx_tenx_test
+Klhl13,2.1153759360560423e-6,1.8812106957951964,0.571,0.112,0.00172403138788567,2,seurat_soupx_tenx_test
+Plxna4,3.873653126433955e-6,-5.784474697359444,0.071,0.748,0.00315702729804367,2,seurat_soupx_tenx_test
+Mrpl39,4.654856767950855e-6,1.9431254785830836,0.786,0.245,0.00379370826587994,2,seurat_soupx_tenx_test
+Tmeff1,5.187569037186392e-6,-2.6384384456762082,0.143,0.829,0.0042278687653069,2,seurat_soupx_tenx_test
+Lgi2,9.3137406692634e-6,3.352516414720785,0.214,0.017,0.00759069864544967,2,seurat_soupx_tenx_test
+Cpxm1,1.3195373184382485e-5,3.352516414720785,0.286,0.035,0.01075422914527172,2,seurat_soupx_tenx_test
+Serf2,1.334505729857521e-5,0.8942775989963212,1,0.958,0.01087622169833879,2,seurat_soupx_tenx_test
+Hivep3,1.549134506773795e-5,-4.694607497393241,0,0.661,0.01262544623020643,2,seurat_soupx_tenx_test
+Ltbp1,1.7031753733147223e-5,1.5780761151359164,0.643,0.157,0.01388087929251498,2,seurat_soupx_tenx_test
+Pdzd11,2.106611067331479e-5,1.86176925561728,0.786,0.392,0.01716888019875155,2,seurat_soupx_tenx_test
+Lrrc57,2.592358581298591e-5,1.9988794601060849,0.571,0.14,0.02112772243758352,2,seurat_soupx_tenx_test
+Mgat5b,3.304398330384083e-5,-4.111007958550395,0,0.626,0.02693084639263028,2,seurat_soupx_tenx_test
+Mmd2,3.3119692099065835e-5,2.0961766614609996,0.857,0.388,0.02699254906073865,2,seurat_soupx_tenx_test
+Vegfb,3.499230972506464e-5,1.850016074191602,0.786,0.301,0.02851873242592768,2,seurat_soupx_tenx_test
+Msmo1,3.79297166004921e-5,1.970467327395852,0.857,0.423,0.03091271902940106,2,seurat_soupx_tenx_test
+Kif26a,4.128498808402059e-5,2.143063049091835,0.429,0.084,0.03364726528847678,2,seurat_soupx_tenx_test
+Rpl13,4.5754276634623855e-5,0.7134561712360101,1,0.997,0.03728973545721844,2,seurat_soupx_tenx_test
+Myt1l,3.3224743516773994e-13,-1.0931254086406694,0.806,0.904,2.70781659661708e-10,0,seurat_soupx_tenx_test
+Mef2c,6.97414600381475e-12,-1.5395844270626693,0.455,0.778,5.683928993109021e-9,0,seurat_soupx_tenx_test
+Rpl13,1.0867220994150292e-11,0.5203315086187699,1,0.993,8.856785110232488e-9,0,seurat_soupx_tenx_test
+Hnrnpa1,8.905311310994811e-11,0.7025446296895241,0.988,0.978,7.257828718460773e-8,0,seurat_soupx_tenx_test
+Fau,2.7536127223539774e-10,0.5149425736872084,1,0.978,2.2441943687184917e-7,0,seurat_soupx_tenx_test
+Rpsa,5.111941824052582e-10,0.7296207435530384,0.988,0.993,4.166232586602854e-7,0,seurat_soupx_tenx_test
+Insm1,6.008487668943348e-9,1.5368064625665037,0.691,0.378,4.896917450188829e-6,0,seurat_soupx_tenx_test
+Cep170,1.7660764019951242e-8,-0.9556764332513308,0.667,0.8,1.439352267626026e-5,0,seurat_soupx_tenx_test
+Rpl26,2.0743783917007455e-8,0.5260304171008894,0.988,1,1.6906183892361076e-5,0,seurat_soupx_tenx_test
+Psmc2,7.159262588086667e-8,1.0355887567710609,0.745,0.481,5.834799009290634e-5,0,seurat_soupx_tenx_test
+Phactr1,2.489795021099361e-7,-0.6952543545565697,0.873,0.933,2.0291829421959791e-4,0,seurat_soupx_tenx_test
+Tmem50a,3.065125547143323e-7,0.9142400513440634,0.739,0.459,2.498077320921808e-4,0,seurat_soupx_tenx_test
+Abr,8.802610933503194e-7,-1.2895066171949847,0.479,0.622,7.174127910805103e-4,0,seurat_soupx_tenx_test
+Hsp90ab1,9.327724336888556e-7,0.4352634190102318,1,1,7.602095334564172e-4,0,seurat_soupx_tenx_test
+Rpl19,1.1936241442328142e-6,0.4251355374926633,1,1,9.728036775497436e-4,0,seurat_soupx_tenx_test
+Plxna4,2.7200977082226347e-6,-1.1180261492506314,0.679,0.763,0.00221687963220144,0,seurat_soupx_tenx_test
+Rian,3.583748668831769e-6,-1.3570699010076193,0.158,0.4,0.00292075516509789,0,seurat_soupx_tenx_test
+Dok5,4.687639742544039e-6,-1.5834203359127508,0.364,0.548,0.00382042639017339,0,seurat_soupx_tenx_test
+Adamts2,7.2580454251312034e-6,-2.0182045953775907,0.085,0.274,0.00591530702148193,0,seurat_soupx_tenx_test
+Snhg14,7.365891068336551e-6,-1.0795835478207536,0.467,0.652,0.00600320122069428,0,seurat_soupx_tenx_test
+Clic4,1.4357499430125536e-5,1.3902341082782712,0.515,0.289,0.01170136203555231,0,seurat_soupx_tenx_test
+Mmd2,1.959820087193392e-5,0.7776075786635521,0.521,0.274,0.01597253371062614,0,seurat_soupx_tenx_test
+Jakmip2,2.236064558441623e-5,-0.8938344427830722,0.558,0.696,0.01822392615129922,0,seurat_soupx_tenx_test
+Rplp2,2.6456989489221488e-5,0.4170247146729893,1,0.978,0.02156244643371551,0,seurat_soupx_tenx_test
+Dpysl2,3.140355593677372e-5,-0.4898510145151511,0.933,0.948,0.02559389808847058,0,seurat_soupx_tenx_test
+Hivep3,3.9823660847893635e-5,-1.023569403458554,0.57,0.704,0.03245628359103331,0,seurat_soupx_tenx_test
diff --git a/tests/run_test_workflow.sh b/tests/run_test_workflow.sh
new file mode 100755
index 0000000..f3136a4
--- /dev/null
+++ b/tests/run_test_workflow.sh
@@ -0,0 +1,74 @@
+#!/usr/bin/env bash
+#SBATCH -p sapphire,shared
+#SBATCH -e testdata_workflow_%A.err
+#SBATCH -o testdata_workflow_%A.out
+#SBATCH -J testdata_workflow
+#SBATCH -N 1
+#SBATCH -c 1
+#SBATCH --mem 8000
+#SBATCH -t 72:00:00
+
+set -euo pipefail
+
+usage() {
+    echo "Usage: $0 [--conda-prefix PATH] [additional snakemake args...]"
+}
+
+script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
+repo_root=$(cd "${script_dir}/.." && pwd)
+cd "${repo_root}"
+
+snakemake_conda_prefix=""
+extra_snakemake_args=()
+
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --conda-prefix)
+            if [[ $# -lt 2 ]]; then
+                usage >&2
+                exit 2
+            fi
+            snakemake_conda_prefix="$2"
+            shift 2
+            ;;
+        -h|--help)
+            usage
+            exit 0
+            ;;
+        *)
+            extra_snakemake_args+=("$1")
+            shift
+            ;;
+    esac
+done
+
+if ! command -v snakemake >/dev/null 2>&1; then
+    echo "snakemake is not available on PATH" >&2
+    exit 127
+fi
+
+common_args=(
+    --snakefile workflow/Snakefile
+    --configfile config/config.yaml
+    --config sampleTable=testdata/samplesheet_test.tsv resultsDir=testdata/results
+    --use-conda
+    --workflow-profile profiles/slurm
+    --profile cannon
+)
+
+conda_prefix_args=()
+if [[ -n "${snakemake_conda_prefix}" ]]; then
+    conda_prefix_args=(--conda-prefix "${snakemake_conda_prefix}")
+fi
+
+snakemake --unlock "${common_args[@]}" "${conda_prefix_args[@]}"
+rm -rf testdata/results
+
+snakemake \
+    "${common_args[@]}" \
+    "${conda_prefix_args[@]}" \
+    --rerun-incomplete \
+    --retries 2 \
+    --jobs 200 \
+    --latency-wait 600 \
+    "${extra_snakemake_args[@]}"
diff --git a/tests/test_cellbender_rule.py b/tests/test_cellbender_rule.py
new file mode 100644
index 0000000..9aa2e4d
--- /dev/null
+++ b/tests/test_cellbender_rule.py
@@ -0,0 +1,127 @@
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+
+
+FAKE_CELLBENDER = r"""#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ "${1:-}" == "remove-background" && "${2:-}" == "--help" ]]; then
+    printf '%s\\n' "cellbender remove-background" "  --seed INTEGER"
+    exit 0
+fi
+
+if [[ "${1:-}" != "remove-background" ]]; then
+    echo "unexpected cellbender invocation: $*" >&2
+    exit 2
+fi
+shift
+
+input=""
+output=""
+while [[ $# -gt 0 ]]; do
+    case "$1" in
+        --input)
+            input="$2"
+            shift 2
+            ;;
+        --output)
+            output="$2"
+            shift 2
+            ;;
+        --seed)
+            shift 2
+            ;;
+        --cuda)
+            shift
+            ;;
+        *)
+            shift
+            ;;
+    esac
+done
+
+if [[ -z "${input}" ]]; then
+    echo "missing --input" >&2
+    exit 3
+fi
+if [[ -z "${output}" ]]; then
+    echo "missing --output" >&2
+    exit 3
+fi
+if [[ ! -s "${input}" ]]; then
+    echo "input does not exist or is empty: ${input}" >&2
+    exit 4
+fi
+
+mkdir -p "$(dirname "${output}")"
+printf 'fake raw cellbender output for %s\\n' "${input}" > "${output}"
+filtered="${output%.h5}_filtered.h5"
+printf 'fake filtered cellbender output for %s\\n' "${input}" > "${filtered}"
+"""
+
+
+def write_fake_cellbender(tmp_path):
+    fake_bin = tmp_path / "bin"
+    fake_bin.mkdir()
+    fake_cellbender = fake_bin / "cellbender"
+    fake_cellbender.write_text(FAKE_CELLBENDER)
+    fake_cellbender.chmod(0o755)
+    return fake_bin
+
+
+def test_cellbender_rule_uses_cellbender_filtered_output_convention(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = repo_root / TEST_SAMPLE_SHEET
+    assert sample_sheet.exists(), f"missing test sample sheet: {sample_sheet}"
+
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    fake_bin = write_fake_cellbender(tmp_path)
+    results_dir = tmp_path / "results"
+    base_output = results_dir / "cellbender" / "cellbender_test.h5"
+    filtered_output = results_dir / "cellbender" / "cellbender_test_filtered.h5"
+
+    env = os.environ.copy()
+    env["PATH"] = f"{fake_bin}{os.pathsep}{env.get('PATH', '')}"
+
+    cmd = [
+        snakemake,
+        str(base_output),
+        str(filtered_output),
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--executor",
+        "local",
+        "--cores",
+        "1",
+        "--latency-wait",
+        "5",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        f"resultsDir={results_dir.as_posix()}",
+    ]
+
+    result = subprocess.run(
+        cmd,
+        cwd=repo_root,
+        env=env,
+        text=True,
+        capture_output=True,
+        check=False,
+    )
+
+    assert result.returncode == 0, result.stdout + result.stderr
+    assert base_output.read_text().startswith("fake raw cellbender output")
+    assert filtered_output.read_text().startswith("fake filtered cellbender output")
diff --git a/tests/test_conda_container_validation.py b/tests/test_conda_container_validation.py
new file mode 100644
index 0000000..ceb5140
--- /dev/null
+++ b/tests/test_conda_container_validation.py
@@ -0,0 +1,245 @@
+import os
+import re
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+import yaml
+
+
+ENV_DIR = Path("workflow/envs")
+RULE_DIR = Path("workflow/rules")
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+EXPECTED_ENV_FILES = {
+    "cellbender.yml",
+    "doubletfinder.yml",
+    "emptydrops.yml",
+    "posthocfilter.yml",
+    "scdblfinder.yml",
+    "soupx.yml",
+    "tenx2seuratrds.yml",
+}
+CONDA_REFERENCE_RE = re.compile(r"conda:\s*\n\s*['\"]\.\./envs/([^'\"]+)['\"]")
+CONTAINER_RE = re.compile(r"container:\s*\n\s*['\"]([^'\"]+)['\"]")
+
+R_IMPORTS_BY_ENV = {
+    "cellbender.yml": ["Seurat", "tidyverse", "bluster"],
+    "doubletfinder.yml": ["Seurat", "tidyverse", "remotes", "fields", "Matrix", "KernSmooth", "ROCR", "igraph", "glmGamPoi", "bluster"],
+    "emptydrops.yml": ["Seurat", "tidyverse", "DropletUtils", "scater", "glmGamPoi", "bluster", "Matrix", "R.utils"],
+    "posthocfilter.yml": ["Seurat", "tidyverse", "glmGamPoi", "scater", "bluster"],
+    "scdblfinder.yml": ["Seurat", "tidyverse", "scDblFinder", "glmGamPoi", "bluster"],
+    "soupx.yml": ["Seurat", "tidyverse", "glmGamPoi", "bluster", "SoupX"],
+    "tenx2seuratrds.yml": ["Seurat", "tidyverse", "scCustomize", "hdf5r", "glmGamPoi", "bluster", "presto"],
+}
+PYTHON_IMPORTS_BY_ENV = {
+    "cellbender.yml": ["cellbender"],
+}
+
+
+def repo_root():
+    return Path(__file__).resolve().parents[1]
+
+
+def read_yaml(path):
+    with path.open() as handle:
+        return yaml.safe_load(handle)
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def run_command(cmd, cwd, env=None, timeout=120):
+    return subprocess.run(
+        cmd,
+        cwd=cwd,
+        env=env,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=timeout,
+    )
+
+
+def available_conda_frontend():
+    requested = os.environ.get("SNAKEMAKE_CONDA_FRONTEND")
+    if requested and shutil.which(requested):
+        return shutil.which(requested)
+    for candidate in ("mamba", "conda"):
+        path = shutil.which(candidate)
+        if path:
+            return path
+    raise AssertionError("neither mamba nor conda is available on PATH")
+
+
+def r_require_namespace_expr(packages):
+    package_vector = ", ".join(repr(package) for package in packages)
+    return (
+        f"packages <- c({package_vector}); "
+        "missing <- packages[!vapply(packages, requireNamespace, logical(1), quietly = TRUE)]; "
+        "if (length(missing)) { stop(paste('missing R packages:', paste(missing, collapse = ',')), call. = FALSE) }"
+    )
+
+
+def test_selected_conda_env_name_is_known(pytestconfig):
+    selected = pytestconfig.getoption("--conda-env-name")
+    if selected is not None:
+        assert selected in EXPECTED_ENV_FILES, f"unknown workflow env requested: {selected}"
+
+
+def test_workflow_conda_env_files_are_well_formed_and_referenced_envs_exist():
+    root = repo_root()
+    env_paths = sorted((root / ENV_DIR).glob("*.yml"))
+    observed = {path.name for path in env_paths}
+    assert observed == EXPECTED_ENV_FILES
+
+    for env_path in env_paths:
+        env = read_yaml(env_path)
+        assert env["channels"] == ["conda-forge", "bioconda"], env_path
+        assert env.get("channel_priority") == "strict", env_path
+        assert env.get("dependencies"), env_path
+
+    referenced = set()
+    for rule_path in sorted((root / RULE_DIR).glob("*.smk")):
+        referenced.update(CONDA_REFERENCE_RE.findall(rule_path.read_text()))
+
+    missing_references = sorted(name for name in referenced if not (root / ENV_DIR / name).exists())
+    assert not missing_references, "rule conda env references are missing: " + ", ".join(missing_references)
+
+
+def test_workflow_container_declarations_are_explicit_and_recognized():
+    root = repo_root()
+    containers = []
+    for rule_path in sorted((root / RULE_DIR).glob("*.smk")):
+        for uri in CONTAINER_RE.findall(rule_path.read_text()):
+            containers.append((rule_path, uri))
+
+    assert containers, "no workflow container declarations found"
+    assert containers == [(root / "workflow/rules/cellbender.smk", "docker://us.gcr.io/broad-dsde-methods/cellbender:latest")]
+    for _, uri in containers:
+        assert uri.startswith("docker://")
+        assert ":" in uri.removeprefix("docker://"), f"container URI is missing a tag: {uri}"
+
+
+@pytest.mark.parametrize("env_name", sorted(EXPECTED_ENV_FILES))
+def test_conda_env_solves_and_key_packages_import(tmp_path, pytestconfig, env_name):
+    if not pytestconfig.getoption("--run-conda-validation"):
+        pytest.skip("use --run-conda-validation to create and import-check workflow conda envs")
+    selected = pytestconfig.getoption("--conda-env-name")
+    if selected is not None and env_name != selected:
+        pytest.skip(f"only validating requested workflow env: {selected}")
+
+    root = repo_root()
+    env_path = root / ENV_DIR / env_name
+    prefix = tmp_path / env_name.removesuffix(".yml")
+    conda = available_conda_frontend()
+
+    create = run_command(
+        [conda, "env", "create", "--yes", "--prefix", str(prefix), "--file", str(env_path)],
+        root,
+        timeout=1800,
+    )
+    assert create.returncode == 0, combined_output(create)
+
+    r_packages = R_IMPORTS_BY_ENV.get(env_name, [])
+    if r_packages:
+        rscript = prefix / "bin" / "Rscript"
+        assert rscript.exists(), f"missing Rscript in {prefix}"
+        imports = run_command([str(rscript), "-e", r_require_namespace_expr(r_packages)], root, timeout=300)
+        assert imports.returncode == 0, combined_output(imports)
+
+    python_packages = PYTHON_IMPORTS_BY_ENV.get(env_name, [])
+    if python_packages:
+        python = prefix / "bin" / "python"
+        assert python.exists(), f"missing python in {prefix}"
+        statements = "; ".join(f"import {package}" for package in python_packages)
+        imports = run_command([str(python), "-c", statements], root, timeout=300)
+        assert imports.returncode == 0, combined_output(imports)
+
+
+def test_cellbender_container_can_be_pulled(tmp_path, pytestconfig):
+    if not pytestconfig.getoption("--run-container-validation"):
+        pytest.skip("use --run-container-validation to pull workflow containers")
+
+    root = repo_root()
+    uri = "docker://us.gcr.io/broad-dsde-methods/cellbender:latest"
+    docker_image = uri.removeprefix("docker://")
+
+    if shutil.which("docker"):
+        result = run_command(["docker", "pull", docker_image], root, timeout=1800)
+    elif shutil.which("apptainer"):
+        result = run_command(["apptainer", "pull", str(tmp_path / "cellbender.sif"), uri], root, timeout=1800)
+    elif shutil.which("singularity"):
+        result = run_command(["singularity", "pull", str(tmp_path / "cellbender.sif"), uri], root, timeout=1800)
+    else:
+        pytest.skip("docker, apptainer, or singularity is required for container validation")
+
+    assert result.returncode == 0, combined_output(result)
+
+
+def test_doubletfinder_github_install_rule_executes(tmp_path, pytestconfig):
+    if not pytestconfig.getoption("--run-doubletfinder-install"):
+        pytest.skip("use --run-doubletfinder-install to test the networked GitHub install rule")
+
+    root = repo_root()
+    sample_sheet = root / TEST_SAMPLE_SHEET
+    assert sample_sheet.exists(), f"missing test sample sheet: {sample_sheet}"
+
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    results_dir = tmp_path / "results"
+    conda_prefix = tmp_path / "snakemake-conda"
+    target = results_dir / "doubletfinder_installed.txt"
+    env = os.environ.copy()
+    conda_frontend = os.environ.get("SNAKEMAKE_CONDA_FRONTEND")
+    if conda_frontend is None and shutil.which("mamba"):
+        conda_frontend = "mamba"
+
+    cmd = [
+        snakemake,
+        str(target),
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--executor",
+        "local",
+        "--cores",
+        "1",
+        "--jobs",
+        "1",
+        "--latency-wait",
+        "30",
+        "--use-conda",
+        "--conda-prefix",
+        str(conda_prefix),
+        "--show-failed-logs",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        f"resultsDir={results_dir.as_posix()}",
+    ]
+    if conda_frontend:
+        cmd.extend(["--conda-frontend", conda_frontend])
+
+    result = run_command(cmd, root, env=env, timeout=1800)
+    assert result.returncode == 0, combined_output(result)
+    assert target.exists(), f"missing DoubletFinder install sentinel: {target}"
+
+    rscript_candidates = sorted(conda_prefix.glob("*/bin/Rscript"))
+    assert rscript_candidates, f"no Snakemake conda Rscript found under {conda_prefix}"
+    import_result = None
+    for rscript in rscript_candidates:
+        import_result = run_command(
+            [str(rscript), "-e", "quit(status = ifelse(requireNamespace('DoubletFinder', quietly = TRUE), 0, 1))"],
+            root,
+            timeout=120,
+        )
+        if import_result.returncode == 0:
+            break
+    assert import_result is not None and import_result.returncode == 0, combined_output(import_result)
diff --git a/tests/test_config_validation.py b/tests/test_config_validation.py
new file mode 100644
index 0000000..bef5076
--- /dev/null
+++ b/tests/test_config_validation.py
@@ -0,0 +1,182 @@
+import copy
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+import yaml
+
+
+CONFIG_FILE = Path("config/config.yaml")
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+REQUIRED_CONFIG_KEYS = {
+    "conda-channel-priority",
+    "sampleTable",
+    "workflow_seed",
+    "emptydrop_removal_methods",
+    "ambient_decon_methods",
+    "doublet_removal_methods",
+    "posthoc_methods",
+    "min_nfeature",
+    "min_ncount",
+    "max_mtdna",
+}
+ALLOWED_EMPTYDROP_METHODS = {"tenx", "emptydrops"}
+ALLOWED_DECON_METHODS = {"soupx", "cellbender_fromraw"}
+ALLOWED_DOUBLET_METHODS = {"doubletfinder", "scdblfinder"}
+ALLOWED_POSTHOC_METHODS = {"threshold", "mad"}
+
+
+def load_default_config(repo_root):
+    with (repo_root / CONFIG_FILE).open() as handle:
+        return yaml.safe_load(handle)
+
+
+def write_config(path, config):
+    with path.open("w") as handle:
+        yaml.safe_dump(config, handle, sort_keys=False)
+    return path
+
+
+def results_dir_path(tmp_path):
+    return tmp_path / "results"
+
+
+def run_snakemake(repo_root, config_file, results_dir, *extra_args):
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    cmd = [
+        snakemake,
+        *extra_args,
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        str(config_file),
+    ]
+    if results_dir is not None:
+        cmd.extend(["--config", f"resultsDir={results_dir}"])
+    return subprocess.run(
+        cmd,
+        cwd=repo_root,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=120,
+    )
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def baseline_test_config(repo_root):
+    config = copy.deepcopy(load_default_config(repo_root))
+    config["sampleTable"] = TEST_SAMPLE_SHEET.as_posix()
+    return config
+
+
+def assert_no_duplicate_values(config, key):
+    values = config[key]
+    assert len(values) == len(set(values)), f"{key} contains duplicates"
+
+
+def test_default_config_has_required_keys_and_valid_values():
+    repo_root = Path(__file__).resolve().parents[1]
+    config = load_default_config(repo_root)
+
+    assert REQUIRED_CONFIG_KEYS <= set(config)
+    assert config["conda-channel-priority"] == "strict"
+    assert isinstance(config["sampleTable"], str) and config["sampleTable"]
+    assert isinstance(config["workflow_seed"], int) and not isinstance(config["workflow_seed"], bool)
+
+    for key, allowed_values in [
+        ("emptydrop_removal_methods", ALLOWED_EMPTYDROP_METHODS),
+        ("ambient_decon_methods", ALLOWED_DECON_METHODS),
+        ("doublet_removal_methods", ALLOWED_DOUBLET_METHODS),
+        ("posthoc_methods", ALLOWED_POSTHOC_METHODS),
+    ]:
+        assert isinstance(config[key], list) and config[key]
+        assert set(config[key]) <= allowed_values
+        assert_no_duplicate_values(config, key)
+
+    assert isinstance(config["min_nfeature"], int) and config["min_nfeature"] > 0
+    assert isinstance(config["min_ncount"], int) and config["min_ncount"] > 0
+    assert isinstance(config["max_mtdna"], (int, float)) and 0 <= config["max_mtdna"] <= 100
+
+
+@pytest.mark.parametrize(
+    "mutate, expected_message, override_results_dir",
+    [
+        (lambda cfg: cfg.pop("posthoc_methods"), "missing required key(s): posthoc_methods", True),
+        (lambda cfg: cfg.update({"posthoc_methods": ["threshold", "bad_method"]}), "posthoc_methods contains invalid value(s): bad_method", True),
+        (lambda cfg: cfg.update({"doublet_removal_methods": ["scdblfinder", "scdblfinder"]}), "doublet_removal_methods contains duplicate value(s): scdblfinder", True),
+        (lambda cfg: cfg.update({"ambient_decon_methods": []}), "ambient_decon_methods must be a non-empty list", True),
+        (lambda cfg: cfg.update({"workflow_seed": "12345"}), "workflow_seed must be an integer", True),
+        (lambda cfg: cfg.update({"min_nfeature": 0}), "min_nfeature must be a positive integer", True),
+        (lambda cfg: cfg.update({"max_mtdna": 101}), "max_mtdna must be a number between 0 and 100", True),
+        (lambda cfg: cfg.update({"resultsDir": ""}), "resultsDir must be a non-empty string", False),
+    ],
+)
+def test_invalid_config_fails_early_with_clear_message(tmp_path, mutate, expected_message, override_results_dir):
+    repo_root = Path(__file__).resolve().parents[1]
+    config = baseline_test_config(repo_root)
+    mutate(config)
+    config_file = write_config(tmp_path / "invalid_config.yaml", config)
+
+    results_dir = results_dir_path(tmp_path) if override_results_dir else None
+    result = run_snakemake(repo_root, config_file, results_dir, "-np")
+    output = combined_output(result)
+
+    assert result.returncode != 0
+    assert "Invalid workflow config" in output
+    assert expected_message in output
+
+
+def run_variant_dry_run(tmp_path, **overrides):
+    repo_root = Path(__file__).resolve().parents[1]
+    config = baseline_test_config(repo_root)
+    config.update(overrides)
+    config_file = write_config(tmp_path / "variant_config.yaml", config)
+    results_dir = results_dir_path(tmp_path)
+    result = run_snakemake(repo_root, config_file, results_dir, "-np")
+    output = combined_output(result)
+    assert result.returncode == 0, output
+    return output, results_dir
+
+
+def test_posthoc_method_variant_changes_rule_all_targets(tmp_path):
+    output, results_dir = run_variant_dry_run(tmp_path, posthoc_methods=["threshold"])
+
+    assert str(results_dir / "posthocfilter" / "seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv") in output
+    assert str(results_dir / "posthocfilter" / "seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test_markergenes.csv") in output
+    assert "seurat_posthocfilt_mad" not in output
+
+
+def test_doublet_method_variant_changes_rule_all_targets(tmp_path):
+    output, results_dir = run_variant_dry_run(tmp_path, doublet_removal_methods=["scdblfinder"])
+
+    assert str(results_dir / "scdblfinder" / "seurat_scdblfinder_soupx_tenx_test_markergenes.csv") in output
+    assert str(results_dir / "scdblfinder" / "seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv") in output
+    assert "seurat_doubletfinder" not in output
+    assert "doubletfinder_installed.txt" not in output
+
+
+def test_decon_method_variant_can_exclude_cellbender_targets(tmp_path):
+    output, results_dir = run_variant_dry_run(tmp_path, ambient_decon_methods=["soupx"])
+
+    assert str(results_dir / "soupx" / "seurat_soupx_tenx_test_markergenes.csv") in output
+    assert str(results_dir / "soupx" / "seurat_soupx_emptydrops_test_markergenes.csv") in output
+    assert "cellbender" not in output
+
+
+def test_emptydrop_method_variant_excludes_emptydrops_specific_targets(tmp_path):
+    output, results_dir = run_variant_dry_run(tmp_path, emptydrop_removal_methods=["tenx"])
+
+    assert str(results_dir / "seurat_filtered" / "filtered_seurat_tenx_test_markergenes.csv") in output
+    assert str(results_dir / "soupx" / "seurat_soupx_tenx_test_markergenes.csv") in output
+    assert "emptydrops" not in output
diff --git a/tests/test_marker_checkpoint_expansion.py b/tests/test_marker_checkpoint_expansion.py
new file mode 100644
index 0000000..4772daa
--- /dev/null
+++ b/tests/test_marker_checkpoint_expansion.py
@@ -0,0 +1,157 @@
+import csv
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+CLUSTERS = ["0", "1", "3"]
+
+
+FAKE_RSCRIPT = r"""#!/usr/bin/env bash
+set -euo pipefail
+
+script="${1:?missing script path}"
+shift
+log="${FAKE_RSCRIPT_LOG:?missing FAKE_RSCRIPT_LOG}"
+
+case "$(basename "${script}")" in
+    find_markers.R)
+        rds="${1:?missing input rds}"
+        cluster="${2:?missing cluster id}"
+        output="${3:?missing output csv}"
+        mkdir -p "$(dirname "${output}")"
+        printf 'find_markers\t%s\t%s\t%s\n' "${cluster}" "${rds}" "${output}" >> "${log}"
+        {
+            printf 'genesymbol,p_val,avg_log2FC,pct.1,pct.2,p_val_adj,cluster,workflow\n'
+            printf 'Gene%s,0.01,1.0,0.5,0.1,0.05,%s,checkpoint_test\n' "${cluster}" "${cluster}"
+        } > "${output}"
+        ;;
+    combine_markers.R)
+        output="${1:?missing output csv}"
+        shift
+        mkdir -p "$(dirname "${output}")"
+        printf 'combine_markers\t%s\n' "$*" >> "${log}"
+        : > "${output}"
+        header_written=0
+        for marker_csv in "$@"; do
+            if [[ "${header_written}" -eq 0 ]]; then
+                cat "${marker_csv}" >> "${output}"
+                header_written=1
+            else
+                tail -n +2 "${marker_csv}" >> "${output}"
+            fi
+        done
+        ;;
+    *)
+        echo "unexpected Rscript target: ${script}" >&2
+        exit 2
+        ;;
+esac
+"""
+
+
+def write_fake_rscript(tmp_path):
+    fake_bin = tmp_path / "bin"
+    fake_bin.mkdir()
+    fake_rscript = fake_bin / "Rscript"
+    fake_rscript.write_text(FAKE_RSCRIPT)
+    fake_rscript.chmod(0o755)
+    return fake_bin
+
+
+def run_command(cmd, repo_root, env):
+    return subprocess.run(
+        cmd,
+        cwd=repo_root,
+        env=env,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=120,
+    )
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def read_marker_rows(path):
+    with path.open(newline="") as handle:
+        return list(csv.DictReader(handle))
+
+
+def test_marker_checkpoint_expands_find_markers_for_materialized_clusters(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = repo_root / TEST_SAMPLE_SHEET
+    assert sample_sheet.exists(), f"missing test sample sheet: {sample_sheet}"
+
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    fake_bin = write_fake_rscript(tmp_path)
+    rscript_log = tmp_path / "fake_rscript.log"
+    results_dir = tmp_path / "results"
+    prefix = Path("checkpoint_marker") / "seurat_checkpoint_marker_test"
+    prefix_path = results_dir / prefix
+    marker_csv = prefix_path.with_name(prefix_path.name + "_markergenes.csv")
+    cluster_ids = prefix_path.with_name(prefix_path.name + "_cluster_ids.txt")
+    input_rds = prefix_path.with_suffix(".rds")
+    manifest_dir = prefix_path.with_name(prefix_path.name + "_marker_manifest")
+
+    prefix_path.parent.mkdir(parents=True)
+    input_rds.write_text("dummy rds path consumed only by fake Rscript\n")
+    cluster_ids.write_text("\n".join(CLUSTERS) + "\n")
+
+    env = os.environ.copy()
+    env["PATH"] = f"{fake_bin}{os.pathsep}{env.get('PATH', '')}"
+    env["FAKE_RSCRIPT_LOG"] = str(rscript_log)
+
+    cmd = [
+        snakemake,
+        str(marker_csv),
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--executor",
+        "local",
+        "--cores",
+        "1",
+        "--jobs",
+        "1",
+        "--latency-wait",
+        "5",
+        "--printshellcmds",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        f"resultsDir={results_dir.as_posix()}",
+    ]
+
+    result = run_command(cmd, repo_root, env)
+    output = combined_output(result)
+    assert result.returncode == 0, output
+    assert "marker_manifest" in output
+    assert "find_markers" in output
+    assert "combine_markers" in output
+
+    rows = read_marker_rows(marker_csv)
+    observed_clusters = sorted(row["cluster"] for row in rows)
+    assert observed_clusters == CLUSTERS
+    assert [row["workflow"] for row in rows] == ["checkpoint_test"] * len(CLUSTERS)
+
+    log_lines = rscript_log.read_text().splitlines()
+    find_lines = [line for line in log_lines if line.startswith("find_markers\t")]
+    combine_lines = [line for line in log_lines if line.startswith("combine_markers\t")]
+    assert sorted(line.split("\t")[1] for line in find_lines) == CLUSTERS
+    assert len(combine_lines) == 1
+    for cluster in CLUSTERS:
+        assert f"_markergenes_cluster{cluster}.csv" in combine_lines[0]
+
+    assert not cluster_ids.exists(), "combine_markers should remove cluster id temp input"
+    assert not manifest_dir.exists(), "combine_markers should remove checkpoint manifest directory"
diff --git a/tests/test_r_rule_execution.py b/tests/test_r_rule_execution.py
new file mode 100644
index 0000000..52603b0
--- /dev/null
+++ b/tests/test_r_rule_execution.py
@@ -0,0 +1,115 @@
+import os
+import shutil
+import subprocess
+from pathlib import Path
+
+
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+VALIDATOR = Path(__file__).with_name("validate_r_rule_outputs.R")
+
+
+def run_command(cmd, repo_root, env=None, timeout=None):
+    return subprocess.run(
+        cmd,
+        cwd=repo_root,
+        env=env,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=timeout,
+    )
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def find_rscript_with_seuratobject(repo_root):
+    candidates = []
+    path_rscript = shutil.which("Rscript")
+    if path_rscript:
+        candidates.append(Path(path_rscript))
+    candidates.extend(sorted((repo_root / ".snakemake" / "conda").glob("*/bin/Rscript")))
+
+    seen = set()
+    for candidate in candidates:
+        if candidate in seen or not candidate.exists():
+            continue
+        seen.add(candidate)
+        result = subprocess.run(
+            [
+                str(candidate),
+                "-e",
+                "quit(status = ifelse(requireNamespace('SeuratObject', quietly = TRUE), 0, 1))",
+            ],
+            text=True,
+            capture_output=True,
+            check=False,
+        )
+        if result.returncode == 0:
+            return candidate
+
+    raise AssertionError("could not find an Rscript with the SeuratObject package installed")
+
+
+def test_tenx_marker_rule_chain_executes_r_scripts_and_produces_valid_outputs(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = repo_root / TEST_SAMPLE_SHEET
+    assert sample_sheet.exists(), f"missing test sample sheet: {sample_sheet}"
+    assert VALIDATOR.exists(), f"missing R output validator: {VALIDATOR}"
+
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    results_dir = tmp_path / "results"
+    seurat_rds = results_dir / "seurat_filtered" / "filtered_seurat_tenx_test.rds"
+    marker_csv = results_dir / "seurat_filtered" / "filtered_seurat_tenx_test_markergenes.csv"
+
+    env = os.environ.copy()
+    env["SCRNASEQ_PREPROCESS_SEED"] = "12345"
+
+    conda_frontend = os.environ.get("SNAKEMAKE_CONDA_FRONTEND")
+    if conda_frontend is None and shutil.which("mamba"):
+        conda_frontend = "mamba"
+
+    cmd = [
+        snakemake,
+        str(marker_csv),
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--executor",
+        "local",
+        "--cores",
+        "1",
+        "--jobs",
+        "1",
+        "--latency-wait",
+        "30",
+        "--use-conda",
+        "--show-failed-logs",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        f"resultsDir={results_dir.as_posix()}",
+    ]
+    if conda_frontend:
+        cmd.extend(["--conda-frontend", conda_frontend])
+
+    result = run_command(cmd, repo_root, env=env, timeout=600)
+    assert result.returncode == 0, combined_output(result)
+    assert seurat_rds.exists(), f"missing Seurat RDS: {seurat_rds}"
+    assert marker_csv.exists(), f"missing marker CSV: {marker_csv}"
+
+    rscript = find_rscript_with_seuratobject(repo_root)
+    validation = run_command(
+        [str(rscript), str(VALIDATOR), str(seurat_rds), str(marker_csv)],
+        repo_root,
+        env=env,
+        timeout=120,
+    )
+    assert validation.returncode == 0, combined_output(validation)
diff --git a/tests/test_reference_output_files.txt b/tests/test_reference_output_files.txt
new file mode 100644
index 0000000..37e2115
--- /dev/null
+++ b/tests/test_reference_output_files.txt
@@ -0,0 +1,52 @@
+testdata/results/cellbender/cellbender_test.h5
+testdata/results/cellbender/cellbender_test_filtered.h5
+testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test.rds
+testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/doubletfinder_installed.txt
+testdata/results/emptydrops/filtered_seurat_emptydrops_test.rds
+testdata/results/emptydrops/filtered_seurat_emptydrops_test_markergenes.csv
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/barcodes.tsv.gz
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/features.tsv.gz
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/matrix.mtx.gz
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/seurat_filtered/filtered_seurat_tenx_test.rds
+testdata/results/seurat_filtered/filtered_seurat_tenx_test_markergenes.csv
+testdata/results/soupx/seurat_soupx_emptydrops_test.rds
+testdata/results/soupx/seurat_soupx_emptydrops_test_markergenes.csv
+testdata/results/soupx/seurat_soupx_tenx_test.rds
+testdata/results/soupx/seurat_soupx_tenx_test_markergenes.csv
diff --git a/tests/test_sample_rule_output_files.txt b/tests/test_sample_rule_output_files.txt
new file mode 100644
index 0000000..460fad6
--- /dev/null
+++ b/tests/test_sample_rule_output_files.txt
@@ -0,0 +1,51 @@
+testdata/results/cellbender/cellbender_test.h5
+testdata/results/cellbender/cellbender_test_filtered.h5
+testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test.rds
+testdata/results/cellbender_fromraw/seurat_cellbender_fromraw_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test.rds
+testdata/results/doubletfinder/seurat_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/emptydrops/filtered_seurat_emptydrops_test.rds
+testdata/results/emptydrops/filtered_seurat_emptydrops_test_markergenes.csv
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/barcodes.tsv.gz
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/features.tsv.gz
+testdata/results/emptydrops/test_emptydrops_filtered_matrix/matrix.mtx.gz
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_mad_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_doubletfinder_soupx_tenx_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test.rds
+testdata/results/posthocfilter/seurat_posthocfilt_threshold_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_emptydrops_test_markergenes.csv
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test.rds
+testdata/results/scdblfinder/seurat_scdblfinder_soupx_tenx_test_markergenes.csv
+testdata/results/seurat_filtered/filtered_seurat_tenx_test.rds
+testdata/results/seurat_filtered/filtered_seurat_tenx_test_markergenes.csv
+testdata/results/soupx/seurat_soupx_emptydrops_test.rds
+testdata/results/soupx/seurat_soupx_emptydrops_test_markergenes.csv
+testdata/results/soupx/seurat_soupx_tenx_test.rds
+testdata/results/soupx/seurat_soupx_tenx_test_markergenes.csv
diff --git a/tests/test_sample_sheet_validation.py b/tests/test_sample_sheet_validation.py
new file mode 100644
index 0000000..f0d179d
--- /dev/null
+++ b/tests/test_sample_sheet_validation.py
@@ -0,0 +1,180 @@
+import shutil
+import subprocess
+from pathlib import Path
+
+
+REQUIRED_TENX_CHILDREN = [
+    "filtered_feature_bc_matrix",
+    "raw_feature_bc_matrix",
+    "raw_feature_bc_matrix.h5",
+]
+
+
+def run_snakemake_with_sample_sheet(repo_root, sample_sheet, results_dir, *extra_args):
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    cmd = [
+        snakemake,
+        *extra_args,
+        "--profile",
+        "none",
+        "--workflow-profile",
+        "none",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={sample_sheet}",
+        f"resultsDir={results_dir}",
+    ]
+    return subprocess.run(
+        cmd,
+        cwd=repo_root,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=120,
+    )
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def write_sample_sheet(path, rows, header="sampleid\ttenx_datadir"):
+    lines = [header]
+    lines.extend(f"{sampleid}\t{tenx_datadir}" for sampleid, tenx_datadir in rows)
+    path.write_text("\n".join(lines) + "\n")
+    return path
+
+
+def test_malformed_sample_sheet_missing_required_column_fails(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = tmp_path / "malformed_samplesheet.tsv"
+    sample_sheet.write_text("sampleid\nmissing_tenx_column\n")
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        tmp_path / "results",
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode != 0
+    assert "Invalid sample sheet" in output
+    assert "missing required column(s): tenx_datadir" in output
+
+
+def test_duplicate_sample_ids_fail_validation(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = write_sample_sheet(
+        tmp_path / "duplicate_samplesheet.tsv",
+        [("duplicate", "testdata"), ("duplicate", "testdata")],
+    )
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        tmp_path / "results",
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode != 0
+    assert "Invalid sample sheet" in output
+    assert "duplicate sampleid value(s): duplicate" in output
+
+
+def test_missing_tenx_datadir_fails_validation(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    missing_data_dir = tmp_path / "does_not_exist"
+    sample_sheet = write_sample_sheet(
+        tmp_path / "missing_data_samplesheet.tsv",
+        [("missing_path", missing_data_dir)],
+    )
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        tmp_path / "results",
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode != 0
+    assert "Invalid sample sheet" in output
+    assert "tenx_datadir does not exist" in output
+    assert str(missing_data_dir) in output
+
+
+def test_incomplete_tenx_datadir_fails_with_missing_required_children(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    incomplete_data_dir = tmp_path / "incomplete_testdata"
+    incomplete_data_dir.mkdir()
+    (incomplete_data_dir / "filtered_feature_bc_matrix").mkdir()
+
+    sample_sheet = write_sample_sheet(
+        tmp_path / "incomplete_data_samplesheet.tsv",
+        [("incomplete", incomplete_data_dir)],
+    )
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        tmp_path / "results",
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode != 0
+    assert "Invalid sample sheet" in output
+    assert "missing raw_feature_bc_matrix" in output
+    assert "missing raw_feature_bc_matrix.h5" in output
+
+
+def test_absolute_tenx_datadir_is_normalized_and_used_for_rule_inputs(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    absolute_testdata = (repo_root / "testdata").resolve()
+    sample_sheet = write_sample_sheet(
+        tmp_path / "absolute_data_samplesheet.tsv",
+        [("absolute_path", absolute_testdata)],
+    )
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        tmp_path / "results",
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode == 0, output
+    for child in REQUIRED_TENX_CHILDREN:
+        assert str(absolute_testdata / child) in output
+
+
+def test_sample_sheet_with_multiple_samples_expands_outputs_for_each_sample(tmp_path):
+    repo_root = Path(__file__).resolve().parents[1]
+    sample_sheet = write_sample_sheet(
+        tmp_path / "multi_sample_samplesheet.tsv",
+        [("test_a", "testdata"), ("test_b", "testdata")],
+    )
+    results_dir = tmp_path / "results"
+
+    result = run_snakemake_with_sample_sheet(
+        repo_root,
+        sample_sheet,
+        results_dir,
+        "-np",
+    )
+    output = combined_output(result)
+
+    assert result.returncode == 0, output
+    for sample_id in ["test_a", "test_b"]:
+        assert f"wildcards: sample={sample_id}" in output
+        assert str(results_dir / "seurat_filtered" / f"filtered_seurat_tenx_{sample_id}_markergenes.csv") in output
+        assert str(results_dir / "cellbender" / f"cellbender_{sample_id}.h5") in output
+        assert str(results_dir / "cellbender" / f"cellbender_{sample_id}_filtered.h5") in output
diff --git a/tests/test_snakemake_dry_run.py b/tests/test_snakemake_dry_run.py
new file mode 100644
index 0000000..c03186c
--- /dev/null
+++ b/tests/test_snakemake_dry_run.py
@@ -0,0 +1,126 @@
+import csv
+import shutil
+import subprocess
+from pathlib import Path
+
+
+
+SAMPLE_ID = "test"
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+RESULTS_DIR = "testdata/results"
+EXPECTED_OUTPUTS = Path(__file__).with_name("test_sample_rule_output_files.txt")
+
+
+def run_snakemake(repo_root, *extra_args):
+    sample_sheet = repo_root / TEST_SAMPLE_SHEET
+    assert sample_sheet.exists(), f"missing test sample sheet: {sample_sheet}"
+
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    cmd = [
+        snakemake,
+        *extra_args,
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        f"resultsDir={RESULTS_DIR}",
+    ]
+    return subprocess.run(
+        cmd,
+        cwd=repo_root,
+        text=True,
+        capture_output=True,
+        check=False,
+    )
+
+
+def combined_output(result):
+    return result.stdout + result.stderr
+
+
+def test_testdata_dag_builds_with_dry_run():
+    repo_root = Path(__file__).resolve().parents[1]
+    result = run_snakemake(repo_root, "-np")
+    output = combined_output(result)
+
+    assert result.returncode == 0, output
+    assert "Building DAG of jobs" in output
+    assert "This was a dry-run" in output
+    for rule_name in [
+        "tenx2seuratrds",
+        "emptydrops",
+        "soupx",
+        "soupx_emptydrops",
+        "cellbender",
+        "cellbender2seurat",
+        "doubletfinder",
+        "scdblfinder",
+        "posthocfilter_threshold",
+        "posthocfilter_mad",
+        "combine_markers",
+    ]:
+        assert rule_name in output
+
+
+def is_internal_workflow_output(output):
+    return (
+        "_markergenes_cluster" in output
+        or output.endswith("_cluster_ids.txt")
+        or output.endswith("_nclusters.txt")
+        or output.endswith("_marker_manifest")
+    )
+
+
+def declared_sample_output_files(summary_text, expected_manifest):
+    lines = summary_text.splitlines()
+    header_index = next(
+        i for i, line in enumerate(lines) if line.startswith("output_file\t")
+    )
+    reader = csv.DictReader(lines[header_index:], delimiter="\t")
+
+    outputs = []
+    for row in reader:
+        output = row["output_file"]
+        if f"_{SAMPLE_ID}" not in output and f"/{SAMPLE_ID}_" not in output:
+            continue
+        if row["status"] == "removed temp file":
+            continue
+        if is_internal_workflow_output(output):
+            continue
+
+        directory_children = [
+            expected
+            for expected in expected_manifest
+            if expected.startswith(f"{output}/")
+        ]
+        if directory_children:
+            outputs.extend(directory_children)
+        else:
+            outputs.append(output)
+
+    return sorted(set(outputs))
+
+
+def test_declared_test_sample_outputs_match_manifest():
+    repo_root = Path(__file__).resolve().parents[1]
+    expected = EXPECTED_OUTPUTS.read_text().splitlines()
+
+    result = run_snakemake(repo_root, "--summary")
+    output = combined_output(result)
+
+    assert result.returncode == 0, output
+
+    observed = declared_sample_output_files(output, expected)
+
+    missing = sorted(set(expected) - set(observed))
+    unexpected = sorted(set(observed) - set(expected))
+
+    assert observed == expected, (
+        "declared outputs differ from manifest\n"
+        f"missing: {missing}\n"
+        f"unexpected: {unexpected}"
+    )
diff --git a/tests/test_snakemake_lint.py b/tests/test_snakemake_lint.py
new file mode 100644
index 0000000..ba252d8
--- /dev/null
+++ b/tests/test_snakemake_lint.py
@@ -0,0 +1,33 @@
+import shutil
+import subprocess
+from pathlib import Path
+
+
+TEST_SAMPLE_SHEET = Path("testdata/samplesheet_test.tsv")
+
+
+def test_snakemake_lint_has_no_findings():
+    repo_root = Path(__file__).resolve().parents[1]
+    snakemake = shutil.which("snakemake")
+    assert snakemake is not None, "snakemake is not available on PATH"
+
+    cmd = [
+        snakemake,
+        "--lint",
+        "--snakefile",
+        "workflow/Snakefile",
+        "--configfile",
+        "config/config.yaml",
+        "--config",
+        f"sampleTable={TEST_SAMPLE_SHEET.as_posix()}",
+        "resultsDir=testdata/results",
+    ]
+    result = subprocess.run(
+        cmd,
+        cwd=repo_root,
+        text=True,
+        capture_output=True,
+        check=False,
+        timeout=120,
+    )
+    assert result.returncode == 0, result.stdout + result.stderr
diff --git a/tests/test_snakemake_workflow_run.py b/tests/test_snakemake_workflow_run.py
new file mode 100644
index 0000000..256f0cc
--- /dev/null
+++ b/tests/test_snakemake_workflow_run.py
@@ -0,0 +1,273 @@
+import csv
+import gzip
+import hashlib
+import math
+import shutil
+import subprocess
+from pathlib import Path
+
+import pytest
+
+
+EXPECTED_OUTPUTS = Path(__file__).with_name("test_sample_rule_output_files.txt")
+REFERENCE_OUTPUTS = Path(__file__).with_name("test_reference_output_files.txt")
+REFERENCE_ROOT = Path(__file__).with_name("reference_outputs")
+SEURAT_METADATA_COMPARATOR = Path(__file__).with_name("compare_seurat_metadata.R")
+MARKER_ABS_TOLERANCE = 1e-8
+MARKER_REL_TOLERANCE = 1e-6
+
+
+def read_manifest(path):
+    return [line.strip() for line in path.read_text().splitlines() if line.strip()]
+
+
+def file_sha256(path):
+    digest = hashlib.sha256()
+    with path.open("rb") as handle:
+        for chunk in iter(lambda: handle.read(1024 * 1024), b""):
+            digest.update(chunk)
+    return digest.hexdigest()
+
+
+def is_seurat_object(path):
+    return path.endswith(".rds")
+
+
+def is_marker_table(path):
+    return path.endswith("_markergenes.csv")
+
+
+def is_emptydrops_matrix_component(path):
+    return "/emptydrops/test_emptydrops_filtered_matrix/" in path and path.endswith(".gz")
+
+
+def is_cellbender_h5(path):
+    return path.startswith("testdata/results/cellbender/") and path.endswith(".h5")
+
+
+def find_rscript_with_seurat(repo_root):
+    candidates = []
+    path_rscript = shutil.which("Rscript")
+    if path_rscript:
+        candidates.append(Path(path_rscript))
+    candidates.extend(sorted((repo_root / ".snakemake" / "conda").glob("*/bin/Rscript")))
+
+    checked = []
+    for candidate in candidates:
+        if candidate in checked or not candidate.exists():
+            continue
+        checked.append(candidate)
+        result = subprocess.run(
+            [
+                str(candidate),
+                "-e",
+                "quit(status = ifelse(requireNamespace('Seurat', quietly = TRUE), 0, 1))",
+            ],
+            text=True,
+            capture_output=True,
+            check=False,
+        )
+        if result.returncode == 0:
+            return candidate
+
+    raise AssertionError("could not find an Rscript with the Seurat package installed")
+
+
+def assert_seurat_metadata_matches(repo_root, paths):
+    if not paths:
+        return
+
+    rscript = find_rscript_with_seurat(repo_root)
+    cmd = [str(rscript), str(SEURAT_METADATA_COMPARATOR)]
+    for rel_path in paths:
+        cmd.extend([str(repo_root / rel_path), str(REFERENCE_ROOT / rel_path)])
+
+    result = subprocess.run(cmd, text=True, capture_output=True, check=False)
+    assert result.returncode == 0, result.stdout + result.stderr
+
+
+def read_csv_table(path):
+    with path.open(newline="") as handle:
+        reader = csv.DictReader(handle)
+        rows = list(reader)
+        return reader.fieldnames or [], rows
+
+
+def numeric_value(value):
+    if value == "":
+        return None
+    try:
+        parsed = float(value)
+    except ValueError:
+        return None
+    if math.isnan(parsed):
+        return None
+    return parsed
+
+
+def assert_marker_value_matches(path, column, current, reference):
+    current_numeric = numeric_value(current)
+    reference_numeric = numeric_value(reference)
+    if current_numeric is not None and reference_numeric is not None:
+        assert math.isclose(
+            current_numeric,
+            reference_numeric,
+            rel_tol=MARKER_REL_TOLERANCE,
+            abs_tol=MARKER_ABS_TOLERANCE,
+        ), (
+            f"{path}: marker value differs for column {column}: "
+            f"{current} != {reference}"
+        )
+        return
+
+    assert current == reference, (
+        f"{path}: marker value differs for column {column}: {current!r} != {reference!r}"
+    )
+
+
+def marker_rows_by_cluster_gene(path, rows):
+    keys = []
+    indexed = {}
+    for row in rows:
+        key = (row.get("cluster"), row.get("genesymbol"))
+        keys.append(key)
+        indexed[key] = row
+
+    assert len(indexed) == len(rows), f"{path}: duplicate cluster/genesymbol rows found"
+    return keys, indexed
+
+
+def assert_marker_tables_match(repo_root, paths):
+    for rel_path in paths:
+        current_path = repo_root / rel_path
+        reference_path = REFERENCE_ROOT / rel_path
+        current_columns, current_rows = read_csv_table(current_path)
+        reference_columns, reference_rows = read_csv_table(reference_path)
+
+        assert current_columns == reference_columns, (
+            f"{rel_path}: marker columns differ\n"
+            f"current: {current_columns}\nreference: {reference_columns}"
+        )
+        assert "cluster" in current_columns, f"{rel_path}: missing cluster column"
+        assert "genesymbol" in current_columns, f"{rel_path}: missing genesymbol column"
+
+        current_keys, current_index = marker_rows_by_cluster_gene(rel_path, current_rows)
+        reference_keys, reference_index = marker_rows_by_cluster_gene(rel_path, reference_rows)
+
+        assert sorted(current_keys) == sorted(reference_keys), (
+            f"{rel_path}: marker genes differ by cluster"
+        )
+
+        for key in sorted(reference_keys):
+            current_row = current_index[key]
+            reference_row = reference_index[key]
+            for column in current_columns:
+                assert_marker_value_matches(
+                    rel_path,
+                    column,
+                    current_row[column],
+                    reference_row[column],
+                )
+
+
+def read_gzip_contents(path):
+    with gzip.open(path, "rb") as handle:
+        return handle.read()
+
+
+def assert_emptydrops_matrix_contents_match(repo_root, paths):
+    for rel_path in paths:
+        current = read_gzip_contents(repo_root / rel_path)
+        reference = read_gzip_contents(REFERENCE_ROOT / rel_path)
+        assert current == reference, f"{rel_path}: decompressed matrix component differs"
+
+
+def assert_h5_contents_match(repo_root, paths):
+    for rel_path in paths:
+        result = subprocess.run(
+            ["h5diff", "-q", str(repo_root / rel_path), str(REFERENCE_ROOT / rel_path)],
+            text=True,
+            capture_output=True,
+            check=False,
+        )
+        assert result.returncode == 0, (
+            f"{rel_path}: HDF5 contents differ\n" + result.stdout + result.stderr
+        )
+
+
+def assert_byte_identical(repo_root, paths):
+    mismatches = []
+    for rel_path in paths:
+        current = repo_root / rel_path
+        reference = REFERENCE_ROOT / rel_path
+        if file_sha256(current) != file_sha256(reference):
+            mismatches.append(rel_path)
+
+    assert not mismatches, (
+        "current outputs differ byte-for-byte from reference outputs:\n"
+        + "\n".join(mismatches[:50])
+    )
+
+
+def assert_current_outputs_match_reference(repo_root):
+    expected = read_manifest(REFERENCE_OUTPUTS)
+
+    missing_current = [path for path in expected if not (repo_root / path).exists()]
+    missing_reference = [
+        path for path in expected if not (REFERENCE_ROOT / path).exists()
+    ]
+    assert not missing_current, (
+        "missing current outputs listed in reference manifest:\n"
+        + "\n".join(missing_current[:50])
+    )
+    assert not missing_reference, (
+        "missing reference outputs listed in reference manifest:\n"
+        + "\n".join(missing_reference[:50])
+    )
+
+    seurat_objects = [path for path in expected if is_seurat_object(path)]
+    marker_tables = [path for path in expected if is_marker_table(path)]
+    matrix_components = [
+        path for path in expected if is_emptydrops_matrix_component(path)
+    ]
+    h5_outputs = [path for path in expected if is_cellbender_h5(path)]
+    byte_identical = [
+        path
+        for path in expected
+        if path not in set(seurat_objects + marker_tables + matrix_components + h5_outputs)
+    ]
+
+    assert_seurat_metadata_matches(repo_root, seurat_objects)
+    assert_marker_tables_match(repo_root, marker_tables)
+    assert_emptydrops_matrix_contents_match(repo_root, matrix_components)
+    assert_h5_contents_match(repo_root, h5_outputs)
+    assert_byte_identical(repo_root, byte_identical)
+
+
+def test_testdata_workflow_run(pytestconfig):
+    if not pytestconfig.getoption("--run-workflow"):
+        pytest.skip("use --run-workflow to run the full workflow on testdata")
+
+    repo_root = Path(__file__).resolve().parents[1]
+    cmd = ["bash", "tests/run_test_workflow.sh"]
+
+    conda_prefix = pytestconfig.getoption("--snakemake-conda-prefix")
+    if conda_prefix:
+        cmd.extend(["--conda-prefix", conda_prefix])
+
+    result = subprocess.run(
+        cmd,
+        cwd=repo_root,
+        text=True,
+        capture_output=True,
+        check=False,
+    )
+
+    assert result.returncode == 0, result.stdout + result.stderr
+
+    expected = read_manifest(EXPECTED_OUTPUTS)
+    missing = [path for path in expected if not (repo_root / path).exists()]
+
+    assert not missing, "missing expected workflow outputs:\n" + "\n".join(missing[:50])
+
+    assert_current_outputs_match_reference(repo_root)
diff --git a/tests/update_reference_outputs.py b/tests/update_reference_outputs.py
new file mode 100755
index 0000000..a701510
--- /dev/null
+++ b/tests/update_reference_outputs.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python3
+import shutil
+from pathlib import Path
+
+
+REPO_ROOT = Path(__file__).resolve().parents[1]
+MANIFEST = Path(__file__).with_name("test_reference_output_files.txt")
+REFERENCE_ROOT = Path(__file__).with_name("reference_outputs")
+
+
+def read_manifest(path):
+    return [line.strip() for line in path.read_text().splitlines() if line.strip()]
+
+
+def main():
+    outputs = read_manifest(MANIFEST)
+    missing = [path for path in outputs if not (REPO_ROOT / path).exists()]
+    if missing:
+        raise SystemExit(
+            "Cannot update reference outputs; missing current outputs:\n"
+            + "\n".join(missing)
+        )
+
+    for rel_path in outputs:
+        source = REPO_ROOT / rel_path
+        target = REFERENCE_ROOT / rel_path
+        target.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copy2(source, target)
+
+    print(f"Copied {len(outputs)} reference output files to {REFERENCE_ROOT}")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/validate_r_rule_outputs.R b/tests/validate_r_rule_outputs.R
new file mode 100644
index 0000000..bb38f25
--- /dev/null
+++ b/tests/validate_r_rule_outputs.R
@@ -0,0 +1,122 @@
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) != 2) {
+    stop("usage: validate_r_rule_outputs.R SEURAT_RDS MARKER_CSV", call. = FALSE)
+}
+
+rds_path <- args[[1]]
+marker_path <- args[[2]]
+
+suppressPackageStartupMessages({
+    library(SeuratObject)
+})
+
+fail <- function(message) {
+    stop(message, call. = FALSE)
+}
+
+if (!file.exists(rds_path) || file.info(rds_path)$size == 0) {
+    fail(paste("missing or empty Seurat RDS:", rds_path))
+}
+if (!file.exists(marker_path) || file.info(marker_path)$size == 0) {
+    fail(paste("missing or empty marker CSV:", marker_path))
+}
+
+obj <- readRDS(rds_path)
+if (!inherits(obj, "Seurat")) {
+    fail(paste("RDS is not a Seurat object; classes:", paste(class(obj), collapse = ",")))
+}
+
+n_features <- nrow(obj)
+n_cells <- ncol(obj)
+if (n_features < 100) {
+    fail(paste("Seurat object has too few features:", n_features))
+}
+if (n_cells < 100) {
+    fail(paste("Seurat object has too few cells:", n_cells))
+}
+
+metadata <- obj@meta.data
+if (nrow(metadata) != n_cells) {
+    fail("metadata row count does not match Seurat cell count")
+}
+if (anyDuplicated(rownames(metadata))) {
+    fail("metadata contains duplicate cell barcodes")
+}
+if (any(is.na(rownames(metadata))) || any(rownames(metadata) == "")) {
+    fail("metadata contains missing or empty cell barcodes")
+}
+
+required_metadata <- c("orig.ident", "nCount_RNA", "nFeature_RNA", "percent.mt", "seurat_clusters")
+missing_metadata <- setdiff(required_metadata, colnames(metadata))
+if (length(missing_metadata) > 0) {
+    fail(paste("metadata missing columns:", paste(missing_metadata, collapse = ",")))
+}
+
+if (any(!is.finite(metadata$nCount_RNA)) || any(metadata$nCount_RNA <= 0)) {
+    fail("metadata nCount_RNA contains non-positive or non-finite values")
+}
+if (any(!is.finite(metadata$nFeature_RNA)) || any(metadata$nFeature_RNA <= 0)) {
+    fail("metadata nFeature_RNA contains non-positive or non-finite values")
+}
+if (any(!is.finite(metadata$percent.mt)) || any(metadata$percent.mt < 0 | metadata$percent.mt > 100)) {
+    fail("metadata percent.mt contains values outside [0, 100]")
+}
+
+cluster_ids <- as.character(metadata$seurat_clusters)
+if (length(unique(cluster_ids)) < 2) {
+    fail("Seurat object has fewer than two clusters")
+}
+
+required_reductions <- c("pca", "umap")
+missing_reductions <- setdiff(required_reductions, names(obj@reductions))
+if (length(missing_reductions) > 0) {
+    fail(paste("Seurat object missing reductions:", paste(missing_reductions, collapse = ",")))
+}
+
+markers <- read.csv(marker_path, stringsAsFactors = FALSE, check.names = FALSE)
+expected_marker_columns <- c("genesymbol", "p_val", "avg_log2FC", "pct.1", "pct.2", "p_val_adj", "cluster", "workflow")
+if (!identical(colnames(markers), expected_marker_columns)) {
+    fail(paste(
+        "marker CSV columns differ; observed:", paste(colnames(markers), collapse = ","),
+        "expected:", paste(expected_marker_columns, collapse = ",")
+    ))
+}
+if (nrow(markers) == 0) {
+    fail("marker CSV has no rows")
+}
+if (any(is.na(markers$genesymbol)) || any(markers$genesymbol == "")) {
+    fail("marker CSV contains missing or empty genesymbol values")
+}
+
+numeric_columns <- c("p_val", "avg_log2FC", "pct.1", "pct.2", "p_val_adj")
+for (column in numeric_columns) {
+    values <- markers[[column]]
+    if (any(!is.finite(values))) {
+        fail(paste("marker CSV column has non-finite values:", column))
+    }
+}
+for (column in c("p_val", "pct.1", "pct.2", "p_val_adj")) {
+    values <- markers[[column]]
+    if (any(values < 0 | values > 1)) {
+        fail(paste("marker CSV column has values outside [0, 1]:", column))
+    }
+}
+
+marker_clusters <- as.character(markers$cluster)
+if (!all(marker_clusters %in% cluster_ids)) {
+    fail("marker CSV contains clusters not present in Seurat metadata")
+}
+if (length(unique(marker_clusters)) < 2) {
+    fail("marker CSV has markers for fewer than two clusters")
+}
+if (!all(markers$workflow == "filtered_seurat_tenx_test")) {
+    fail("marker CSV workflow column does not match filtered_seurat_tenx_test")
+}
+
+cat(sprintf(
+    "validated R rule outputs: %d features, %d cells, %d marker rows, %d clusters\n",
+    n_features,
+    n_cells,
+    nrow(markers),
+    length(unique(cluster_ids))
+))
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 1403532..44b8d5e 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -1,32 +1,111 @@
 import pandas as pd
-import os
 import yaml
 
-sampleinfo = pd.read_table(config["sampleTable"],dtype={"sampleid": str})
+include: "rules/common.smk"
 
-SAMPLES=list(sampleinfo.loc[:,"sampleid"])
+validated_config = validate_workflow_config(config)
+sampleinfo = pd.read_table(config["sampleTable"], dtype={"sampleid": str})
+sampleinfo = validate_sample_sheet(sampleinfo, config["sampleTable"])
+
+SAMPLES = list(sampleinfo.loc[:, "sampleid"])
 
 with open("profiles/slurm/config.yaml") as f:
     slurm_profile_config = yaml.safe_load(f)
 
-DECON_METHODS = config["ambient_decon_methods"]
-DOUBLET_METHODS = config["doublet_removal_methods"]
-EMPTYDROP_METHODS = config["emptydrop_removal_methods"]
-POSTHOC_METHODS = config["posthoc_methods"]
+DECON_METHODS = validated_config["decon_methods"]
+DOUBLET_METHODS = validated_config["doublet_methods"]
+EMPTYDROP_METHODS = validated_config["emptydrop_methods"]
+POSTHOC_METHODS = validated_config["posthoc_methods"]
+RESULTS_DIR = config.get("resultsDir", "results").rstrip("/")
+WORKFLOW_SEED = int(config["workflow_seed"])
+
+TENX_TARGETS = expand(
+    f"{RESULTS_DIR}/seurat_filtered/filtered_seurat_tenx_{{sample}}_markergenes.csv",
+    sample=SAMPLES,
+)
+EMPTYDROPS_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/emptydrops/filtered_seurat_emptydrops_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+    )
+    if "emptydrops" in EMPTYDROP_METHODS
+    else []
+)
+SOUPX_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/soupx/seurat_soupx_{{empty_method}}_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+        empty_method=EMPTYDROP_METHODS,
+    )
+    if "soupx" in DECON_METHODS
+    else []
+)
+CELLBENDER_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+    )
+    if "cellbender_fromraw" in DECON_METHODS
+    else []
+)
+SOUPX_DOUBLET_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_soupx_{{empty_method}}_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+        doublet_method=DOUBLET_METHODS,
+        empty_method=EMPTYDROP_METHODS,
+    )
+    if "soupx" in DECON_METHODS
+    else []
+)
+CELLBENDER_DOUBLET_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_cellbender_fromraw_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+        doublet_method=DOUBLET_METHODS,
+    )
+    if "cellbender_fromraw" in DECON_METHODS
+    else []
+)
+SOUPX_POSTHOC_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_{{posthoc_method}}_{{doublet_method}}_soupx_{{empty_method}}_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+        posthoc_method=POSTHOC_METHODS,
+        doublet_method=DOUBLET_METHODS,
+        empty_method=EMPTYDROP_METHODS,
+    )
+    if "soupx" in DECON_METHODS
+    else []
+)
+CELLBENDER_POSTHOC_TARGETS = (
+    expand(
+        f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_{{posthoc_method}}_{{doublet_method}}_cellbender_fromraw_{{sample}}_markergenes.csv",
+        sample=SAMPLES,
+        posthoc_method=POSTHOC_METHODS,
+        doublet_method=DOUBLET_METHODS,
+    )
+    if "cellbender_fromraw" in DECON_METHODS
+    else []
+)
+ALL_TARGETS = (
+    TENX_TARGETS
+    + EMPTYDROPS_TARGETS
+    + SOUPX_TARGETS
+    + CELLBENDER_TARGETS
+    + SOUPX_DOUBLET_TARGETS
+    + CELLBENDER_DOUBLET_TARGETS
+    + SOUPX_POSTHOC_TARGETS
+    + CELLBENDER_POSTHOC_TARGETS
+)
 
 default_target: True
 
 
 rule all:
     input:
-        expand("results/seurat_filtered/filtered_seurat_tenx_" + "{sample}" + "_markergenes.csv",sample=SAMPLES),
-        expand("results/emptydrops/filtered_seurat_emptydrops_{sample}_markergenes.csv",sample=SAMPLES),  
-        expand("results/soupx/seurat_soupx_{empty_method}_" + "{sample}" + "_markergenes.csv",sample=SAMPLES,empty_method=EMPTYDROP_METHODS),
-        expand("results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}_markergenes.csv",sample=SAMPLES),
-        expand("results/{doublet_method}/seurat_{doublet_method}_soupx_{empty_method}_{sample}_markergenes.csv",sample=SAMPLES,doublet_method=DOUBLET_METHODS,empty_method=EMPTYDROP_METHODS),
-        expand("results/{doublet_method}/seurat_{doublet_method}_cellbender_fromraw_{sample}_markergenes.csv",sample=SAMPLES,doublet_method=DOUBLET_METHODS),
-        expand("results/posthocfilter/seurat_posthocfilt_{posthoc_method}_{doublet_method}_cellbender_fromraw_{sample}_markergenes.csv",sample=SAMPLES,posthoc_method=POSTHOC_METHODS,doublet_method=DOUBLET_METHODS),
-        expand("results/posthocfilter/seurat_posthocfilt_{posthoc_method}_{doublet_method}_soupx_{empty_method}_{sample}_markergenes.csv",sample=SAMPLES,posthoc_method=POSTHOC_METHODS,doublet_method=DOUBLET_METHODS,empty_method=EMPTYDROP_METHODS)
+        ALL_TARGETS
+
 
 include: "rules/tenx2seuratrds.smk"
 include: "rules/soupx.smk"
diff --git a/workflow/envs/cellbender.yml b/workflow/envs/cellbender.yml
index 2437bc9..da1aef2 100644
--- a/workflow/envs/cellbender.yml
+++ b/workflow/envs/cellbender.yml
@@ -2,6 +2,8 @@ channels:
  - conda-forge
  - bioconda
 
+channel_priority: strict
+
 dependencies:
   - r-tidyverse
   - python=3.9  
diff --git a/workflow/rules/cellbender.smk b/workflow/rules/cellbender.smk
index 5c3f9c0..5b9d8de 100644
--- a/workflow/rules/cellbender.smk
+++ b/workflow/rules/cellbender.smk
@@ -1,21 +1,15 @@
-def input_function(wildcards):
-    tenx_dir = sampleinfo.loc[
-        sampleinfo["sampleid"] == wildcards.sample,
-        "tenx_datadir"
-    ].values[0]
-    input_path = os.path.join(tenx_dir, "raw_feature_bc_matrix.h5")
-    return input_path
-
-
 rule cellbender:
     input:
-        input_function
+        tenx_raw_h5_input
     output:
-        base     = "results/cellbender/cellbender_{sample}.h5",
-        filtered = "results/cellbender/cellbender_{sample}_filtered.h5"
+        base=f"{RESULTS_DIR}/cellbender/cellbender_{{sample}}.h5",
+        filtered=f"{RESULTS_DIR}/cellbender/cellbender_{{sample}}_filtered.h5"
+    log:
+        f"{RESULTS_DIR}/logs/cellbender/cellbender_{{sample}}.log"
     params:
         # per-sample directory ONLY for checkpoints / temp
-        workdir = "scratch/cellbender/{sample}"
+        workdir="scratch/cellbender/{sample}",
+        seed=WORKFLOW_SEED
     container:
         "docker://us.gcr.io/broad-dsde-methods/cellbender:latest"
     resources:
@@ -25,21 +19,51 @@ rule cellbender:
         runtime = 2880
     shell:
         r"""
+        set -euo pipefail
+
         # base_dir is the directory from which Snakemake was launched
+        exec > {log} 2>&1
         base_dir=$(pwd)
+        export PYTHONHASHSEED={params.seed}
+
+        seed_args=()
+        if cellbender remove-background --help 2>&1 | grep -q -- "--seed"; then
+            seed_args=(--seed {params.seed})
+        fi
+
+        input_h5="{input}"
+        case "${{input_h5}}" in
+            /*) ;;
+            *) input_h5="${{base_dir}}/${{input_h5}}" ;;
+        esac
+
+        base_output="{output.base}"
+        case "${{base_output}}" in
+            /*) ;;
+            *) base_output="${{base_dir}}/${{base_output}}" ;;
+        esac
+
+        filtered_output="{output.filtered}"
+        case "${{filtered_output}}" in
+            /*) ;;
+            *) filtered_output="${{base_dir}}/${{filtered_output}}" ;;
+        esac
+
+        expected_filtered_output="${{base_output%.h5}}_filtered.h5"
+        if [ "${{expected_filtered_output}}" != "${{filtered_output}}" ]; then
+            echo "CellBender derives filtered output from --output as ${{expected_filtered_output}}, but the rule declares ${{filtered_output}}" >&2
+            exit 1
+        fi
 
         # Make sure output and scratch dirs exist on the host
-        mkdir -p "$(dirname "{output.base}")"
+        mkdir -p "$(dirname "${{base_output}}")"
         mkdir -p "{params.workdir}"
 
-        # Run cellbender in the per-sample scratch dir so ckpt.tar.gz is unique
+        # Run CellBender in the per-sample scratch dir so ckpt.tar.gz is unique.
         cd "{params.workdir}"
 
-        cellbender remove-background \
-            --cuda \
-            --input "{input}" \
-            --output "${{base_dir}}/{output.base}"
+        cellbender remove-background             --cuda             "${{seed_args[@]}}"             --input "${{input_h5}}"             --output "${{base_output}}"
 
-        # If you actually generate a separate filtered file, add that command here,
-        # and ensure it writes to ${{base_dir}}/{output.filtered}
+        test -s "${{base_output}}"
+        test -s "${{filtered_output}}"
         """
diff --git a/workflow/rules/cellbender2seurat.smk b/workflow/rules/cellbender2seurat.smk
index b41dc8b..4a536cc 100644
--- a/workflow/rules/cellbender2seurat.smk
+++ b/workflow/rules/cellbender2seurat.smk
@@ -1,18 +1,22 @@
 rule cellbender2seurat:
     input:
-        data="results/cellbender/cellbender_{sample}_filtered.h5",
+        data=f"{RESULTS_DIR}/cellbender/cellbender_{{sample}}_filtered.h5",
         script="workflow/scripts/cellbender2seurat.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-         rds="results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}.rds",
-         nclusters=temp("results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}_nclusters.txt"),
-         cluster_ids=temp("results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/cellbender2seurat/cellbender2seurat_{{sample}}.log"
     conda:
         "../envs/tenx2seuratrds.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
new file mode 100644
index 0000000..023708c
--- /dev/null
+++ b/workflow/rules/common.smk
@@ -0,0 +1,189 @@
+import os
+from pathlib import Path
+
+
+REQUIRED_CONFIG_KEYS = {
+    "conda-channel-priority",
+    "sampleTable",
+    "workflow_seed",
+    "emptydrop_removal_methods",
+    "ambient_decon_methods",
+    "doublet_removal_methods",
+    "posthoc_methods",
+    "min_nfeature",
+    "min_ncount",
+    "max_mtdna",
+}
+ALLOWED_EMPTYDROP_METHODS = {"tenx", "emptydrops"}
+ALLOWED_DECON_METHODS = {"soupx", "cellbender_fromraw"}
+ALLOWED_DOUBLET_METHODS = {"doubletfinder", "scdblfinder"}
+ALLOWED_POSTHOC_METHODS = {"threshold", "mad"}
+
+
+def require_non_empty_string(config_values, key, errors):
+    value = config_values.get(key)
+    if not isinstance(value, str) or not value.strip():
+        errors.append(f"{key} must be a non-empty string")
+
+
+def require_positive_int(config_values, key, errors):
+    value = config_values.get(key)
+    if isinstance(value, bool) or not isinstance(value, int) or value <= 0:
+        errors.append(f"{key} must be a positive integer")
+
+
+def validate_method_list(config_values, key, allowed_values, errors):
+    value = config_values.get(key)
+    if not isinstance(value, list) or not value:
+        errors.append(f"{key} must be a non-empty list")
+        return []
+
+    normalized = []
+    for item in value:
+        if not isinstance(item, str) or not item.strip():
+            errors.append(f"{key} contains a non-string or empty value")
+            continue
+        normalized.append(item)
+
+    duplicates = sorted({item for item in normalized if normalized.count(item) > 1})
+    if duplicates:
+        errors.append(f"{key} contains duplicate value(s): " + ", ".join(duplicates))
+
+    invalid = sorted(set(normalized) - allowed_values)
+    if invalid:
+        errors.append(
+            f"{key} contains invalid value(s): "
+            + ", ".join(invalid)
+            + "; allowed values are: "
+            + ", ".join(sorted(allowed_values))
+        )
+
+    return normalized
+
+
+def validate_workflow_config(config_values):
+    errors = []
+    missing_keys = sorted(REQUIRED_CONFIG_KEYS - set(config_values.keys()))
+    if missing_keys:
+        errors.append("missing required key(s): " + ", ".join(missing_keys))
+
+    require_non_empty_string(config_values, "sampleTable", errors)
+    if config_values.get("conda-channel-priority") != "strict":
+        errors.append("conda-channel-priority must be 'strict'")
+
+    workflow_seed = config_values.get("workflow_seed")
+    if isinstance(workflow_seed, bool) or not isinstance(workflow_seed, int):
+        errors.append("workflow_seed must be an integer")
+
+    emptydrop_methods = validate_method_list(config_values, "emptydrop_removal_methods", ALLOWED_EMPTYDROP_METHODS, errors)
+    decon_methods = validate_method_list(config_values, "ambient_decon_methods", ALLOWED_DECON_METHODS, errors)
+    doublet_methods = validate_method_list(config_values, "doublet_removal_methods", ALLOWED_DOUBLET_METHODS, errors)
+    posthoc_methods = validate_method_list(config_values, "posthoc_methods", ALLOWED_POSTHOC_METHODS, errors)
+
+    require_positive_int(config_values, "min_nfeature", errors)
+    require_positive_int(config_values, "min_ncount", errors)
+    max_mtdna = config_values.get("max_mtdna")
+    if isinstance(max_mtdna, bool) or not isinstance(max_mtdna, (int, float)) or not 0 <= max_mtdna <= 100:
+        errors.append("max_mtdna must be a number between 0 and 100")
+
+    if "resultsDir" in config_values:
+        require_non_empty_string(config_values, "resultsDir", errors)
+
+    if errors:
+        raise ValueError("Invalid workflow config: " + "; ".join(errors))
+
+    return {
+        "emptydrop_methods": emptydrop_methods,
+        "decon_methods": decon_methods,
+        "doublet_methods": doublet_methods,
+        "posthoc_methods": posthoc_methods,
+    }
+
+
+REQUIRED_SAMPLE_COLUMNS = {"sampleid", "tenx_datadir"}
+REQUIRED_TENX_PATHS = (
+    "filtered_feature_bc_matrix",
+    "raw_feature_bc_matrix",
+    "raw_feature_bc_matrix.h5",
+)
+
+
+def resolve_tenx_datadir(path_value):
+    path = Path(str(path_value)).expanduser()
+    if not path.is_absolute():
+        path = Path.cwd() / path
+    return path
+
+
+def validate_sample_sheet(sampleinfo, sample_table):
+    errors = []
+    missing_columns = sorted(REQUIRED_SAMPLE_COLUMNS - set(sampleinfo.columns))
+    if missing_columns:
+        errors.append("missing required column(s): " + ", ".join(missing_columns))
+        raise ValueError(f"Invalid sample sheet {sample_table}: " + "; ".join(errors))
+
+    if sampleinfo.empty:
+        errors.append("sample sheet has no rows")
+
+    sample_ids = sampleinfo["sampleid"].astype("string")
+    missing_sample_ids = sampleinfo.index[sample_ids.isna() | (sample_ids.str.strip() == "")].tolist()
+    if missing_sample_ids:
+        errors.append("sampleid is missing or empty on row(s): " + ", ".join(str(i + 2) for i in missing_sample_ids))
+
+    duplicate_sample_ids = sorted(sample_ids[sample_ids.duplicated(keep=False)].dropna().unique())
+    if duplicate_sample_ids:
+        errors.append("duplicate sampleid value(s): " + ", ".join(duplicate_sample_ids))
+
+    data_dirs = sampleinfo["tenx_datadir"].astype("string")
+    missing_data_dirs = sampleinfo.index[data_dirs.isna() | (data_dirs.str.strip() == "")].tolist()
+    if missing_data_dirs:
+        errors.append("tenx_datadir is missing or empty on row(s): " + ", ".join(str(i + 2) for i in missing_data_dirs))
+
+    if errors:
+        raise ValueError(f"Invalid sample sheet {sample_table}: " + "; ".join(errors))
+
+    resolved_data_dirs = []
+    for row_number, (sample_id, data_dir_value) in enumerate(zip(sample_ids, data_dirs), start=2):
+        data_dir = resolve_tenx_datadir(data_dir_value)
+        resolved_data_dirs.append(str(data_dir))
+        if not data_dir.exists():
+            errors.append(f"sample {sample_id} row {row_number}: tenx_datadir does not exist: {data_dir}")
+            continue
+        for required_path in REQUIRED_TENX_PATHS:
+            candidate = data_dir / required_path
+            if not candidate.exists():
+                errors.append(f"sample {sample_id} row {row_number}: missing {required_path}: {candidate}")
+
+    if errors:
+        raise ValueError(f"Invalid sample sheet {sample_table}: " + "; ".join(errors))
+
+    validated = sampleinfo.copy()
+    validated["sampleid"] = sample_ids.astype(str)
+    validated["tenx_datadir"] = resolved_data_dirs
+    return validated
+
+
+def sample_tenx_dir(wildcards):
+    return sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
+
+
+def tenx_filtered_matrix_input(wildcards):
+    return os.path.join(sample_tenx_dir(wildcards), "filtered_feature_bc_matrix")
+
+
+def tenx_raw_matrix_input(wildcards):
+    return os.path.join(sample_tenx_dir(wildcards), "raw_feature_bc_matrix")
+
+
+def tenx_raw_h5_input(wildcards):
+    return os.path.join(sample_tenx_dir(wildcards), "raw_feature_bc_matrix.h5")
+
+
+def marker_chunk_inputs(wildcards):
+    manifest_dir = checkpoints.marker_manifest.get(prefix=wildcards.prefix).output.manifest
+    cluster_ids = glob_wildcards(str(Path(manifest_dir) / "{cluster}.txt")).cluster
+    return expand(
+        f"{RESULTS_DIR}/{{prefix}}_markergenes_cluster{{cluster}}.csv",
+        prefix=wildcards.prefix,
+        cluster=cluster_ids,
+    )
diff --git a/workflow/rules/doubletfinder.smk b/workflow/rules/doubletfinder.smk
index cb0e802..9eb8431 100644
--- a/workflow/rules/doubletfinder.smk
+++ b/workflow/rules/doubletfinder.smk
@@ -1,13 +1,15 @@
 rule doubletfinder:
     input:
-        install_validation="results/doubletfinder_installed.txt",
-        data="results/{decon_method}/seurat_{decon_method}_{empty_method}_{sample}.rds",
+        install_validation=f"{RESULTS_DIR}/doubletfinder_installed.txt",
+        data=f"{RESULTS_DIR}/{{decon_method}}/seurat_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
         script="workflow/scripts/doubletfinder.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/doubletfinder/seurat_doubletfinder_{decon_method}_{empty_method}_{sample}.rds",
-        nclusters=temp("results/doubletfinder/seurat_doubletfinder_{decon_method}_{empty_method}_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/doubletfinder/seurat_doubletfinder_{decon_method}_{empty_method}_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_{{decon_method}}_{{empty_method}}_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_{{decon_method}}_{{empty_method}}_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/doubletfinder/doubletfinder_{{decon_method}}_{{empty_method}}_{{sample}}.log"
     conda:
         "../envs/doubletfinder.yml"
     wildcard_constraints:
@@ -16,28 +18,34 @@ rule doubletfinder:
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
 
 
 rule doubletfinder_cellbender:
     input:
-        install_validation="results/doubletfinder_installed.txt",
-        data="results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}.rds",
+        install_validation=f"{RESULTS_DIR}/doubletfinder_installed.txt",
+        data=f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}.rds",
         script="workflow/scripts/doubletfinder.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{sample}.rds",
-        nclusters=temp("results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/doubletfinder/seurat_doubletfinder_cellbender_fromraw_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/doubletfinder/doubletfinder_cellbender_fromraw_{{sample}}.log"
     conda:
         "../envs/doubletfinder.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/emptydrops.smk b/workflow/rules/emptydrops.smk
index 408a72e..10825bc 100644
--- a/workflow/rules/emptydrops.smk
+++ b/workflow/rules/emptydrops.smk
@@ -1,24 +1,23 @@
-def input_function(wildcards):
-    tenx_dir = sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
-    input_path = os.path.join(tenx_dir, "raw_feature_bc_matrix")
-    return input_path
-
 rule emptydrops:
     input:
-        data=input_function,
+        data=tenx_raw_matrix_input,
         script="workflow/scripts/emptydrops.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        seurat="results/emptydrops/filtered_seurat_emptydrops_{sample}.rds",
-        matrixdir=directory("results/emptydrops/{sample}_emptydrops_filtered_matrix"),
-        nclusters=temp("results/emptydrops/filtered_seurat_emptydrops_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/emptydrops/filtered_seurat_emptydrops_{sample}_cluster_ids.txt")
+        seurat=f"{RESULTS_DIR}/emptydrops/filtered_seurat_emptydrops_{{sample}}.rds",
+        matrixdir=directory(f"{RESULTS_DIR}/emptydrops/{{sample}}_emptydrops_filtered_matrix"),
+        nclusters=temp(f"{RESULTS_DIR}/emptydrops/filtered_seurat_emptydrops_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/emptydrops/filtered_seurat_emptydrops_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/emptydrops/emptydrops_{{sample}}.log"
     conda:
         "../envs/emptydrops.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.seurat} {output.matrixdir} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.seurat} {output.matrixdir} {output.nclusters} {output.cluster_ids} {wildcards.sample} > {log} 2>&1
         """
diff --git a/workflow/rules/install_doubletfinder.smk b/workflow/rules/install_doubletfinder.smk
index c451a89..4c5b95c 100644
--- a/workflow/rules/install_doubletfinder.smk
+++ b/workflow/rules/install_doubletfinder.smk
@@ -1,12 +1,14 @@
 localrules: install_doubletfinder
 
 rule install_doubletfinder:
-  output:
-    "results/doubletfinder_installed.txt"
-  conda:
-    "../envs/doubletfinder.yml"
-  shell:
-    """
-    Rscript -e "remotes::install_github('chris-mcginnis-ucsf/DoubletFinder', force = TRUE)"
-    touch {output}
-    """
+    output:
+        f"{RESULTS_DIR}/doubletfinder_installed.txt"
+    log:
+        f"{RESULTS_DIR}/logs/install_doubletfinder.log"
+    conda:
+        "../envs/doubletfinder.yml"
+    shell:
+        """
+        Rscript -e "remotes::install_github('chris-mcginnis-ucsf/DoubletFinder', force = TRUE)" > {log} 2>&1
+        touch {output}
+        """
diff --git a/workflow/rules/markers.smk b/workflow/rules/markers.smk
index b604d7a..3897ace 100644
--- a/workflow/rules/markers.smk
+++ b/workflow/rules/markers.smk
@@ -1,51 +1,34 @@
-from pathlib import Path
-
-
-def read_cluster_ids(cluster_ids_path):
-    with open(cluster_ids_path) as handle:
-        return [line.strip() for line in handle if line.strip()]
-
-
 checkpoint marker_manifest:
     input:
-        cluster_ids="results/{prefix}_cluster_ids.txt"
+        cluster_ids=f"{RESULTS_DIR}/{{prefix}}_cluster_ids.txt"
     output:
-        manifest=temp(directory("results/{prefix}_marker_manifest"))
-    run:
-        manifest_dir = Path(output.manifest)
-        manifest_dir.mkdir(parents=True, exist_ok=True)
-
-        for existing_path in manifest_dir.iterdir():
-            if existing_path.is_file():
-                existing_path.unlink()
-
-        for cluster_id in read_cluster_ids(input.cluster_ids):
-            (manifest_dir / f"{cluster_id}.txt").write_text(f"{cluster_id}\n")
-
-
-def marker_chunk_inputs(wildcards):
-    manifest_dir = checkpoints.marker_manifest.get(prefix=wildcards.prefix).output.manifest
-    cluster_ids = glob_wildcards(str(Path(manifest_dir) / "{cluster}.txt")).cluster
-    return expand(
-        "results/{prefix}_markergenes_cluster{cluster}.csv",
-        prefix=wildcards.prefix,
-        cluster=cluster_ids
-    )
+        manifest=temp(directory(f"{RESULTS_DIR}/{{prefix}}_marker_manifest"))
+    log:
+        f"{RESULTS_DIR}/logs/markers/{{prefix}}_marker_manifest.log"
+    conda:
+        "../envs/tenx2seuratrds.yml"
+    script:
+        "../scripts/write_marker_manifest.py"
 
 
 rule find_markers:
     input:
-        rds="results/{prefix}.rds",
-        script="workflow/scripts/find_markers.R"
+        rds=f"{RESULTS_DIR}/{{prefix}}.rds",
+        script="workflow/scripts/find_markers.R",
+        helper="workflow/scripts/silhouette_utils.R"
     output:
-        temp("results/{prefix}_markergenes_cluster{cluster}.csv")
+        temp(f"{RESULTS_DIR}/{{prefix}}_markergenes_cluster{{cluster}}.csv")
+    log:
+        f"{RESULTS_DIR}/logs/markers/{{prefix}}_markergenes_cluster{{cluster}}.log"
     conda:
         "../envs/tenx2seuratrds.yml"
     resources:
         mem_mb=lambda wildcards, attempt: int(12000 * (2 ** (attempt - 1))),
         runtime=lambda wildcards, attempt: int(240 * (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
-        "Rscript {input.script} {input.rds} {wildcards.cluster} {output}"
+        "SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.rds} {wildcards.cluster} {output} > {log} 2>&1"
 
 
 rule combine_markers:
@@ -53,16 +36,23 @@ rule combine_markers:
         markers=marker_chunk_inputs,
         script="workflow/scripts/combine_markers.R"
     output:
-        "results/{prefix}_markergenes.csv"
+        f"{RESULTS_DIR}/{{prefix}}_markergenes.csv"
+    log:
+        f"{RESULTS_DIR}/logs/markers/{{prefix}}_combine_markers.log"
     conda:
         "../envs/tenx2seuratrds.yml"
     resources:
         mem_mb=lambda wildcards, attempt: int(4000 * (2 ** (attempt - 1))),
         runtime=lambda wildcards, attempt: int(60 * (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED,
+        cluster_ids=lambda wildcards: f"{RESULTS_DIR}/{wildcards.prefix}_cluster_ids.txt",
+        nclusters=lambda wildcards: f"{RESULTS_DIR}/{wildcards.prefix}_nclusters.txt",
+        manifest=lambda wildcards: f"{RESULTS_DIR}/{wildcards.prefix}_marker_manifest"
     shell:
         """
-        Rscript {input.script} {output} {input.markers}
-        rm -f results/{wildcards.prefix}_cluster_ids.txt
-        rm -f results/{wildcards.prefix}_nclusters.txt
-        rm -rf results/{wildcards.prefix}_marker_manifest
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {output} {input.markers} > {log} 2>&1
+        rm -f {params.cluster_ids}
+        rm -f {params.nclusters}
+        rm -rf {params.manifest}
         """
diff --git a/workflow/rules/posthocfilter_mad.smk b/workflow/rules/posthocfilter_mad.smk
index 9b9ed86..53c84ae 100644
--- a/workflow/rules/posthocfilter_mad.smk
+++ b/workflow/rules/posthocfilter_mad.smk
@@ -1,13 +1,14 @@
 rule posthocfilter_mad:
     input:
-        data="results/{doublet_method}/seurat_{doublet_method}_{decon_method}_{empty_method}_{sample}.rds",
+        data=f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
         script="workflow/scripts/posthocfilter_mad.R",
         helper="workflow/scripts/silhouette_utils.R"
-
     output:
-        rds="results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_{decon_method}_{empty_method}_{sample}.rds",
-        nclusters=temp("results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_{decon_method}_{empty_method}_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_{decon_method}_{empty_method}_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/posthocfilter/posthocfilter_mad_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.log"
     conda:
         "../envs/posthocfilter.yml"
     wildcard_constraints:
@@ -17,20 +18,25 @@ rule posthocfilter_mad:
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
 
 
 rule posthocfilter_mad_cellbender:
     input:
-        data="results/{doublet_method}/seurat_{doublet_method}_cellbender_fromraw_{sample}.rds",
-        script="workflow/scripts/posthocfilter_mad.R"
+        data=f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_cellbender_fromraw_{{sample}}.rds",
+        script="workflow/scripts/posthocfilter_mad.R",
+        helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_cellbender_fromraw_{sample}.rds",
-        nclusters=temp("results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_cellbender_fromraw_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/posthocfilter/seurat_posthocfilt_mad_{doublet_method}_cellbender_fromraw_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_cellbender_fromraw_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_cellbender_fromraw_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_mad_{{doublet_method}}_cellbender_fromraw_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/posthocfilter/posthocfilter_mad_{{doublet_method}}_cellbender_fromraw_{{sample}}.log"
     conda:
         "../envs/posthocfilter.yml"
     wildcard_constraints:
@@ -38,7 +44,9 @@ rule posthocfilter_mad_cellbender:
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/posthocfilter_threshold.smk b/workflow/rules/posthocfilter_threshold.smk
index 2d08bce..4d4c1e0 100644
--- a/workflow/rules/posthocfilter_threshold.smk
+++ b/workflow/rules/posthocfilter_threshold.smk
@@ -1,13 +1,14 @@
 rule posthocfilter_threshold:
     input:
-        data="results/{doublet_method}/seurat_{doublet_method}_{decon_method}_{empty_method}_{sample}.rds",
+        data=f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
         script="workflow/scripts/posthocfilter_threshold.R",
         helper="workflow/scripts/silhouette_utils.R"
-
     output:
-        rds="results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_{decon_method}_{empty_method}_{sample}.rds",
-        nclusters=temp("results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_{decon_method}_{empty_method}_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_{decon_method}_{empty_method}_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/posthocfilter/posthocfilter_threshold_{{doublet_method}}_{{decon_method}}_{{empty_method}}_{{sample}}.log"
     conda:
         "../envs/posthocfilter.yml"
     wildcard_constraints:
@@ -20,22 +21,25 @@ rule posthocfilter_threshold:
     params:
         min_numfeatures = config["min_nfeature"],
         min_umicount = config["min_ncount"],
-        max_mtdna_pcent = config["max_mtdna"]
+        max_mtdna_pcent = config["max_mtdna"],
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script}  {input.data} {output.rds} \
-        {params.min_numfeatures} {params.min_umicount} {params.max_mtdna_pcent} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script}  {input.data} {output.rds}         {params.min_numfeatures} {params.min_umicount} {params.max_mtdna_pcent} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
 
 
 rule posthocfilter_threshold_cellbender:
     input:
-        data="results/{doublet_method}/seurat_{doublet_method}_cellbender_fromraw_{sample}.rds",
-        script="workflow/scripts/posthocfilter_threshold.R"
+        data=f"{RESULTS_DIR}/{{doublet_method}}/seurat_{{doublet_method}}_cellbender_fromraw_{{sample}}.rds",
+        script="workflow/scripts/posthocfilter_threshold.R",
+        helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_cellbender_fromraw_{sample}.rds",
-        nclusters=temp("results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_cellbender_fromraw_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/posthocfilter/seurat_posthocfilt_threshold_{doublet_method}_cellbender_fromraw_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_cellbender_fromraw_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_cellbender_fromraw_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/posthocfilter/seurat_posthocfilt_threshold_{{doublet_method}}_cellbender_fromraw_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/posthocfilter/posthocfilter_threshold_{{doublet_method}}_cellbender_fromraw_{{sample}}.log"
     conda:
         "../envs/posthocfilter.yml"
     wildcard_constraints:
@@ -46,9 +50,9 @@ rule posthocfilter_threshold_cellbender:
     params:
         min_numfeatures = config["min_nfeature"],
         min_umicount = config["min_ncount"],
-        max_mtdna_pcent = config["max_mtdna"]
+        max_mtdna_pcent = config["max_mtdna"],
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script}  {input.data} {output.rds} \
-        {params.min_numfeatures} {params.min_umicount} {params.max_mtdna_pcent} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script}  {input.data} {output.rds}         {params.min_numfeatures} {params.min_umicount} {params.max_mtdna_pcent} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/scdblfinder.smk b/workflow/rules/scdblfinder.smk
index d3765ec..e63e807 100644
--- a/workflow/rules/scdblfinder.smk
+++ b/workflow/rules/scdblfinder.smk
@@ -1,12 +1,14 @@
 rule scdblfinder:
     input:
-        data="results/{decon_method}/seurat_{decon_method}_{empty_method}_{sample}.rds",
+        data=f"{RESULTS_DIR}/{{decon_method}}/seurat_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
         script="workflow/scripts/scdblfinder.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/scdblfinder/seurat_scdblfinder_{decon_method}_{empty_method}_{sample}.rds",
-        nclusters=temp("results/scdblfinder/seurat_scdblfinder_{decon_method}_{empty_method}_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/scdblfinder/seurat_scdblfinder_{decon_method}_{empty_method}_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_{{decon_method}}_{{empty_method}}_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_{{decon_method}}_{{empty_method}}_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_{{decon_method}}_{{empty_method}}_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/scdblfinder/scdblfinder_{{decon_method}}_{{empty_method}}_{{sample}}.log"
     conda:
         "../envs/scdblfinder.yml"
     wildcard_constraints:
@@ -15,27 +17,33 @@ rule scdblfinder:
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
 
 
 rule scdblfinder_cellbender:
     input:
-        data="results/cellbender_fromraw/seurat_cellbender_fromraw_{sample}.rds",
+        data=f"{RESULTS_DIR}/cellbender_fromraw/seurat_cellbender_fromraw_{{sample}}.rds",
         script="workflow/scripts/scdblfinder.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{sample}.rds",
-        nclusters=temp("results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{sample}_nclusters.txt"),
-        cluster_ids=temp("results/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{sample}_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/scdblfinder/seurat_scdblfinder_cellbender_fromraw_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/scdblfinder/scdblfinder_cellbender_fromraw_{{sample}}.log"
     conda:
         "../envs/scdblfinder.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/soupx.smk b/workflow/rules/soupx.smk
index 4fb698e..2a3a431 100644
--- a/workflow/rules/soupx.smk
+++ b/workflow/rules/soupx.smk
@@ -1,31 +1,24 @@
-def input_function_filtered(wildcards):
-    tenx_dir = sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
-    input_path = os.path.join(tenx_dir, "filtered_feature_bc_matrix")
-    return input_path
-
-def input_function_raw(wildcards):
-    tenx_dir = sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
-    input_path = os.path.join(tenx_dir, "raw_feature_bc_matrix")
-    return input_path
-
-
 rule soupx:
     input:
-        raw=input_function_raw,
-        filtered =  input_function_filtered,
-        seurat_base =  "results/seurat_filtered/filtered_seurat_tenx_" + "{sample}" + ".rds",
+        raw=tenx_raw_matrix_input,
+        filtered=tenx_filtered_matrix_input,
+        seurat_base=f"{RESULTS_DIR}/seurat_filtered/filtered_seurat_tenx_{{sample}}.rds",
         script="workflow/scripts/soupx.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/soupx/seurat_soupx_tenx_" + "{sample}" + ".rds",
-        nclusters=temp("results/soupx/seurat_soupx_tenx_" + "{sample}" + "_nclusters.txt"),
-        cluster_ids=temp("results/soupx/seurat_soupx_tenx_" + "{sample}" + "_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/soupx/seurat_soupx_tenx_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/soupx/seurat_soupx_tenx_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/soupx/seurat_soupx_tenx_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/soupx/soupx_tenx_{{sample}}.log"
     conda:
         "../envs/soupx.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.filtered} {input.raw} {input.seurat_base} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.filtered} {input.raw} {input.seurat_base} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/soupx_emptydrops.smk b/workflow/rules/soupx_emptydrops.smk
index 18e0260..3bc9869 100644
--- a/workflow/rules/soupx_emptydrops.smk
+++ b/workflow/rules/soupx_emptydrops.smk
@@ -1,26 +1,24 @@
-def input_function_raw(wildcards):
-    tenx_dir = sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
-    input_path = os.path.join(tenx_dir, "raw_feature_bc_matrix")
-    return input_path
-
-
 rule soupx_emptydrops:
     input:
-        raw=input_function_raw,
-        filtered = "results/emptydrops/{sample}_emptydrops_filtered_matrix",
-        seurat_base = "results/emptydrops/filtered_seurat_emptydrops_{sample}.rds",
+        raw=tenx_raw_matrix_input,
+        filtered=f"{RESULTS_DIR}/emptydrops/{{sample}}_emptydrops_filtered_matrix",
+        seurat_base=f"{RESULTS_DIR}/emptydrops/filtered_seurat_emptydrops_{{sample}}.rds",
         script="workflow/scripts/soupx.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/soupx/seurat_soupx_emptydrops_" + "{sample}" + ".rds",
-        nclusters=temp("results/soupx/seurat_soupx_emptydrops_" + "{sample}" + "_nclusters.txt"),
-        cluster_ids=temp("results/soupx/seurat_soupx_emptydrops_" + "{sample}" + "_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/soupx/seurat_soupx_emptydrops_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/soupx/seurat_soupx_emptydrops_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/soupx/seurat_soupx_emptydrops_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/soupx/soupx_emptydrops_{{sample}}.log"
     conda:
         "../envs/soupx.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
+    params:
+        seed=WORKFLOW_SEED
     shell:
         """
-        Rscript {input.script} {input.filtered} {input.raw} {input.seurat_base} {output.rds} {output.nclusters} {output.cluster_ids}
+        SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.filtered} {input.raw} {input.seurat_base} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1
         """
diff --git a/workflow/rules/tenx2seuratrds.smk b/workflow/rules/tenx2seuratrds.smk
index 0406426..fa5ab8a 100644
--- a/workflow/rules/tenx2seuratrds.smk
+++ b/workflow/rules/tenx2seuratrds.smk
@@ -1,23 +1,20 @@
-def input_function(wildcards):
-    tenx_dir = sampleinfo.loc[sampleinfo["sampleid"] == wildcards.sample, "tenx_datadir"].values[0]
-    input_path = os.path.join(tenx_dir, "filtered_feature_bc_matrix")
-    print(f"Input path for sample {wildcards.sample}: {input_path}")
-    return input_path
-
 rule tenx2seuratrds:
     input:
-        data=input_function,
+        data=tenx_filtered_matrix_input,
         script="workflow/scripts/tenx2seuratrds.R",
         helper="workflow/scripts/silhouette_utils.R"
     output:
-        rds="results/seurat_filtered/filtered_seurat_tenx_" + "{sample}" + ".rds",
-        nclusters=temp("results/seurat_filtered/filtered_seurat_tenx_" + "{sample}" + "_nclusters.txt"),
-        cluster_ids=temp("results/seurat_filtered/filtered_seurat_tenx_" + "{sample}" + "_cluster_ids.txt")
+        rds=f"{RESULTS_DIR}/seurat_filtered/filtered_seurat_tenx_{{sample}}.rds",
+        nclusters=temp(f"{RESULTS_DIR}/seurat_filtered/filtered_seurat_tenx_{{sample}}_nclusters.txt"),
+        cluster_ids=temp(f"{RESULTS_DIR}/seurat_filtered/filtered_seurat_tenx_{{sample}}_cluster_ids.txt")
+    log:
+        f"{RESULTS_DIR}/logs/tenx2seuratrds/tenx2seuratrds_{{sample}}.log"
     conda:
         "../envs/tenx2seuratrds.yml"
     resources:
         mem_mb = lambda wildcards, attempt: int(24000 * (2 ** (attempt - 1))),
         runtime = lambda wildcards, attempt: int(480* (2 ** (attempt - 1)))
-        
+    params:
+        seed=WORKFLOW_SEED
     shell:
-        "Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids}"
+        "SCRNASEQ_PREPROCESS_SEED={params.seed} Rscript {input.script} {input.data} {output.rds} {output.nclusters} {output.cluster_ids} > {log} 2>&1"
diff --git a/workflow/scripts/cellbender2seurat.R b/workflow/scripts/cellbender2seurat.R
index d957e21..3400be9 100644
--- a/workflow/scripts/cellbender2seurat.R
+++ b/workflow/scripts/cellbender2seurat.R
@@ -9,6 +9,7 @@ library("scCustomize")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -23,11 +24,11 @@ write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_out
 mat <- Read_CellBender_h5_Mat(cellbender_h5)
 seurat <- CreateSeuratObject(mat)
 seurat[["percent.mt"]] <- PercentageFeatureSet(seurat, pattern = "(?i)^mt-")
-seurat <- SCTransform(seurat, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat <- RunPCA(seurat, verbose = FALSE)
-seurat <- RunUMAP(seurat, dims = 1:30)
+seurat <- SCTransform(seurat, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat <- RunPCA(seurat, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat <- RunUMAP(seurat, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat <- FindNeighbors(seurat, dims = 1:30)
-seurat <- FindClusters(seurat)
+seurat <- FindClusters(seurat, random.seed = WORKFLOW_SEED)
 seurat <- add_silhouette_to_metadata(seurat)
 saveRDS(seurat,file=output)
 write_cluster_metadata(seurat, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/doubletfinder.R b/workflow/scripts/doubletfinder.R
index 8711afa..98ad1de 100644
--- a/workflow/scripts/doubletfinder.R
+++ b/workflow/scripts/doubletfinder.R
@@ -10,6 +10,7 @@ library("igraph")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -23,6 +24,7 @@ write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_out
 
 seurat <- readRDS(seurat)
 
+set.seed(WORKFLOW_SEED)
 sweep.res.list <- paramSweep(seurat, PCs = 1:10, sct = TRUE)
 sweep.stats <- summarizeSweep(sweep.res.list, GT = FALSE)
 bcmvn <- find.pK(sweep.stats)
@@ -35,6 +37,7 @@ nExp_poi <- round(0.15*nrow(seurat@meta.data))
 homotypic.prop <- modelHomotypic(seurat$seurat_clusters)
 nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop))
 
+set.seed(WORKFLOW_SEED)
 seurat <- doubletFinder(seurat, PCs = 1:10, pN = 0.25,
                                  pK = optimal_pk, nExp = nExp_poi.adj,
                                  reuse.pANN = NULL,
@@ -46,11 +49,11 @@ rm(seurat)
 gc()
 
 seurat_singlets[["percent.mt"]] <- PercentageFeatureSet(seurat_singlets, pattern = "(?i)^mt-")
-seurat_singlets <- SCTransform(seurat_singlets, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_singlets <- RunPCA(seurat_singlets, verbose = FALSE)
-seurat_singlets <- RunUMAP(seurat_singlets, dims = 1:30)
+seurat_singlets <- SCTransform(seurat_singlets, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_singlets <- RunPCA(seurat_singlets, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_singlets <- RunUMAP(seurat_singlets, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_singlets <- FindNeighbors(seurat_singlets, dims = 1:30)
-seurat_singlets <- FindClusters(seurat_singlets)
+seurat_singlets <- FindClusters(seurat_singlets, random.seed = WORKFLOW_SEED)
 seurat_singlets <- add_silhouette_to_metadata(seurat_singlets)
 
 saveRDS(seurat_singlets,file=output)
diff --git a/workflow/scripts/emptydrops.R b/workflow/scripts/emptydrops.R
index 5188b16..5ac7d5d 100644
--- a/workflow/scripts/emptydrops.R
+++ b/workflow/scripts/emptydrops.R
@@ -4,6 +4,7 @@ seurat_output <- args[2]
 matrix_outdir <- args[3]
 nclusters_output <- args[4]
 cluster_ids_output <- args[5]
+sample_id <- if (length(args) >= 6 && nzchar(args[6])) args[6] else basename(normalizePath(raw, mustWork = FALSE))
 
 library("Seurat")
 library("DropletUtils")
@@ -13,6 +14,7 @@ library("glmGamPoi")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -32,12 +34,14 @@ library("R.utils")
 droputil_rawdata <-read10xCounts(raw)
 colnames(droputil_rawdata) <- droputil_rawdata$Barcode
 rownames(droputil_rawdata) <- make.unique(rowData(droputil_rawdata)$Symbol)
+set.seed(WORKFLOW_SEED)
 dropletutils_out <-emptyDrops(counts(droputil_rawdata))
 is.cell <-!is.na(dropletutils_out$FDR) & dropletutils_out$FDR<0.01
 cell_barcodes <- colnames(droputil_rawdata)[which(is.cell)]
 droputil_filtered <- droputil_rawdata[,is.cell]
 droputil_filtered <- logNormCounts(droputil_filtered)
 seurat_droputil_filtered <- as.Seurat(droputil_filtered, counts = "counts",data="logcounts")
+seurat_droputil_filtered$Sample <- sample_id
 cm <- counts(droputil_filtered)
 if (!inherits(cm, "dgCMatrix")) {
     cm <- as(cm, "dgCMatrix")
@@ -48,11 +52,11 @@ rm(droputil_rawdata, dropletutils_out, droputil_filtered, is.cell, cell_barcodes
 gc()
 seurat_droputil_filtered <- RenameAssays(seurat_droputil_filtered,originalexp="RNA")
 seurat_droputil_filtered[["percent.mt"]] <- PercentageFeatureSet(seurat_droputil_filtered, pattern = "(?i)^mt-")
-seurat_droputil_filtered <- SCTransform(seurat_droputil_filtered, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_droputil_filtered <- RunPCA(seurat_droputil_filtered, verbose = FALSE)
-seurat_droputil_filtered <- RunUMAP(seurat_droputil_filtered, dims = 1:30)
+seurat_droputil_filtered <- SCTransform(seurat_droputil_filtered, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_droputil_filtered <- RunPCA(seurat_droputil_filtered, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_droputil_filtered <- RunUMAP(seurat_droputil_filtered, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_droputil_filtered <- FindNeighbors(seurat_droputil_filtered, dims = 1:30)
-seurat_droputil_filtered <- FindClusters(seurat_droputil_filtered)
+seurat_droputil_filtered <- FindClusters(seurat_droputil_filtered, random.seed = WORKFLOW_SEED)
 seurat_droputil_filtered <- add_silhouette_to_metadata(seurat_droputil_filtered)
 saveRDS(seurat_droputil_filtered,file=seurat_output)
 write_cluster_metadata(seurat_droputil_filtered, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/find_markers.R b/workflow/scripts/find_markers.R
index 47c0337..573bafb 100644
--- a/workflow/scripts/find_markers.R
+++ b/workflow/scripts/find_markers.R
@@ -9,9 +9,13 @@ library("tools")
 
 options(future.globals.maxSize = 16 * 1024^3)
 
+source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
+
 seurat_obj <- readRDS(rds_input)
 Idents(seurat_obj) <- "seurat_clusters"
 
+set.seed(WORKFLOW_SEED)
 markers <- FindMarkers(seurat_obj, ident.1 = cluster_id)
 markers_tbl <- markers %>%
   as.data.frame() %>%
diff --git a/workflow/scripts/posthocfilter_mad.R b/workflow/scripts/posthocfilter_mad.R
index a558699..eed8c92 100644
--- a/workflow/scripts/posthocfilter_mad.R
+++ b/workflow/scripts/posthocfilter_mad.R
@@ -11,6 +11,7 @@ library("scater")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -34,11 +35,11 @@ cells_to_keep <- colnames(seurat)[!discard]
 seurat_filtered<- subset(seurat, cells = cells_to_keep)
 
 seurat_filtered[["percent.mt"]] <- PercentageFeatureSet(seurat_filtered, pattern = "(?i)^mt-")
-seurat_filtered <- SCTransform(seurat_filtered, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_filtered <- RunPCA(seurat_filtered, verbose = FALSE)
-seurat_filtered <- RunUMAP(seurat_filtered, dims = 1:30)
+seurat_filtered <- SCTransform(seurat_filtered, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_filtered <- RunPCA(seurat_filtered, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_filtered <- RunUMAP(seurat_filtered, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_filtered <- FindNeighbors(seurat_filtered, dims = 1:30)
-seurat_filtered <- FindClusters(seurat_filtered)
+seurat_filtered <- FindClusters(seurat_filtered, random.seed = WORKFLOW_SEED)
 seurat_filtered <- add_silhouette_to_metadata(seurat_filtered)
 saveRDS(seurat_filtered,file=filtered_output)
 write_cluster_metadata(seurat_filtered, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/posthocfilter_threshold.R b/workflow/scripts/posthocfilter_threshold.R
index 71d9db1..1680d5f 100644
--- a/workflow/scripts/posthocfilter_threshold.R
+++ b/workflow/scripts/posthocfilter_threshold.R
@@ -14,6 +14,7 @@ library("scater")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -29,11 +30,11 @@ seurat <- readRDS(seurat)
 
 seurat_filtered <- subset(seurat, subset = nFeature_RNA > min_nfeature & nCount_RNA > min_ncount & percent.mt < max_mtdna)
 
-seurat_filtered <- SCTransform(seurat_filtered, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_filtered <- RunPCA(seurat_filtered, verbose = FALSE)
-seurat_filtered <- RunUMAP(seurat_filtered, dims = 1:30)
+seurat_filtered <- SCTransform(seurat_filtered, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_filtered <- RunPCA(seurat_filtered, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_filtered <- RunUMAP(seurat_filtered, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_filtered <- FindNeighbors(seurat_filtered, dims = 1:30)
-seurat_filtered <- FindClusters(seurat_filtered)
+seurat_filtered <- FindClusters(seurat_filtered, random.seed = WORKFLOW_SEED)
 seurat_filtered <- add_silhouette_to_metadata(seurat_filtered)
 saveRDS(seurat_filtered,file=filtered_output)
 write_cluster_metadata(seurat_filtered, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/scdblfinder.R b/workflow/scripts/scdblfinder.R
index 490794d..e4bd4fa 100644
--- a/workflow/scripts/scdblfinder.R
+++ b/workflow/scripts/scdblfinder.R
@@ -10,6 +10,7 @@ library("scDblFinder")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -23,7 +24,8 @@ write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_out
 
 seurat <- readRDS(seurat)
 sce <- as.SingleCellExperiment(seurat)
-sce <- scDblFinder(sce)
+set.seed(WORKFLOW_SEED)
+sce <- scDblFinder(sce, BPPARAM = BiocParallel::SerialParam())
 seurat$scDblFinder.class <- colData(sce)$scDblFinder.class
 rm(sce)
 gc()
@@ -31,11 +33,11 @@ seurat_singlets <- subset(seurat, subset = scDblFinder.class == "singlet")
 rm(seurat)
 gc()
 seurat_singlets[["percent.mt"]] <- PercentageFeatureSet(seurat_singlets, pattern = "(?i)^mt-")
-seurat_singlets <- SCTransform(seurat_singlets, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_singlets <- RunPCA(seurat_singlets, verbose = FALSE)
-seurat_singlets <- RunUMAP(seurat_singlets, dims = 1:30)
+seurat_singlets <- SCTransform(seurat_singlets, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_singlets <- RunPCA(seurat_singlets, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_singlets <- RunUMAP(seurat_singlets, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_singlets <- FindNeighbors(seurat_singlets, dims = 1:30)
-seurat_singlets <- FindClusters(seurat_singlets)
+seurat_singlets <- FindClusters(seurat_singlets, random.seed = WORKFLOW_SEED)
 seurat_singlets <- add_silhouette_to_metadata(seurat_singlets)
 saveRDS(seurat_singlets,file=output)
 write_cluster_metadata(seurat_singlets, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/silhouette_utils.R b/workflow/scripts/silhouette_utils.R
index 747f105..9bd1a4a 100644
--- a/workflow/scripts/silhouette_utils.R
+++ b/workflow/scripts/silhouette_utils.R
@@ -1,3 +1,12 @@
+set_workflow_seed <- function(seed = Sys.getenv("SCRNASEQ_PREPROCESS_SEED", "12345")) {
+  seed <- suppressWarnings(as.integer(seed))
+  if (length(seed) != 1 || is.na(seed)) {
+    stop("SCRNASEQ_PREPROCESS_SEED must be an integer")
+  }
+  set.seed(seed)
+  seed
+}
+
 add_silhouette_to_metadata <- function(
     seurat_obj,
     cluster_col = "seurat_clusters",
diff --git a/workflow/scripts/soupx.R b/workflow/scripts/soupx.R
index 59946a4..163fcdb 100644
--- a/workflow/scripts/soupx.R
+++ b/workflow/scripts/soupx.R
@@ -13,6 +13,7 @@ library("SoupX")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -36,17 +37,18 @@ soup_channel <- SoupX::setClusters(soup_channel,
                                    clusters = as.factor(Idents(seurat_base)))
 soup_channel <- setDR(soup_channel, 
                 DR=Seurat::Embeddings(seurat_base, "umap"))
+set.seed(WORKFLOW_SEED)
 soup_channel <- autoEstCont(soup_channel)
 corrected_counts <- adjustCounts(soup_channel,roundToInt=TRUE)
 seurat_soupx <- CreateSeuratObject(counts = corrected_counts)
 rm(filtered_matrix, raw_matrix, seurat_base, soup_channel, corrected_counts)
 gc()
 seurat_soupx[["percent.mt"]] <- PercentageFeatureSet(seurat_soupx, pattern = "(?i)^mt-")
-seurat_soupx <- SCTransform(seurat_soupx, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_soupx <- RunPCA(seurat_soupx, verbose = FALSE)
-seurat_soupx <- RunUMAP(seurat_soupx, dims = 1:30)
+seurat_soupx <- SCTransform(seurat_soupx, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_soupx <- RunPCA(seurat_soupx, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_soupx <- RunUMAP(seurat_soupx, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_soupx <- FindNeighbors(seurat_soupx, dims = 1:30)
-seurat_soupx <- FindClusters(seurat_soupx)
+seurat_soupx <- FindClusters(seurat_soupx, random.seed = WORKFLOW_SEED)
 seurat_soupx <- add_silhouette_to_metadata(seurat_soupx)
 saveRDS(seurat_soupx,file=output)
 write_cluster_metadata(seurat_soupx, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/tenx2seuratrds.R b/workflow/scripts/tenx2seuratrds.R
index 78a3d00..747708b 100644
--- a/workflow/scripts/tenx2seuratrds.R
+++ b/workflow/scripts/tenx2seuratrds.R
@@ -10,6 +10,7 @@ library("glmGamPoi")
 options(future.globals.maxSize = 16 * 1024^3)
 
 source("workflow/scripts/silhouette_utils.R")
+WORKFLOW_SEED <- set_workflow_seed()
 
 write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_output) {
   cluster_ids <- levels(Idents(seurat_obj))
@@ -24,11 +25,11 @@ write_cluster_metadata <- function(seurat_obj, nclusters_output, cluster_ids_out
 filtered_loaded <- Seurat::Read10X(filtered)
 seurat_obj <- CreateSeuratObject(counts = filtered_loaded)
 seurat_obj[["percent.mt"]] <- PercentageFeatureSet(seurat_obj, pattern = "(?i)^mt-")
-seurat_obj <- SCTransform(seurat_obj, vars.to.regress = "percent.mt", verbose = FALSE)
-seurat_obj <- RunPCA(seurat_obj, verbose = FALSE)
-seurat_obj <- RunUMAP(seurat_obj, dims = 1:30)
+seurat_obj <- SCTransform(seurat_obj, vars.to.regress = "percent.mt", seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_obj <- RunPCA(seurat_obj, seed.use = WORKFLOW_SEED, verbose = FALSE)
+seurat_obj <- RunUMAP(seurat_obj, dims = 1:30, seed.use = WORKFLOW_SEED)
 seurat_obj <- FindNeighbors(seurat_obj, dims = 1:30)
-seurat_obj <- FindClusters(seurat_obj)
+seurat_obj <- FindClusters(seurat_obj, random.seed = WORKFLOW_SEED)
 seurat_obj <- add_silhouette_to_metadata(seurat_obj)
 saveRDS(seurat_obj,file=output)
 write_cluster_metadata(seurat_obj, nclusters_output, cluster_ids_output)
diff --git a/workflow/scripts/write_marker_manifest.py b/workflow/scripts/write_marker_manifest.py
new file mode 100644
index 0000000..ed8cd19
--- /dev/null
+++ b/workflow/scripts/write_marker_manifest.py
@@ -0,0 +1,17 @@
+from pathlib import Path
+
+
+def read_cluster_ids(cluster_ids_path):
+    with open(cluster_ids_path) as handle:
+        return [line.strip() for line in handle if line.strip()]
+
+
+manifest_dir = Path(snakemake.output.manifest)
+manifest_dir.mkdir(parents=True, exist_ok=True)
+
+for existing_path in manifest_dir.iterdir():
+    if existing_path.is_file():
+        existing_path.unlink()
+
+for cluster_id in read_cluster_ids(snakemake.input.cluster_ids):
+    (manifest_dir / f"{cluster_id}.txt").write_text(f"{cluster_id}\\n")