From 0408174db7f97e7903a163823c0fc575855b4e7f Mon Sep 17 00:00:00 2001
From: Adam Freedman <adamfreedman@fas.harvard.edu>
Date: Wed, 10 Jun 2026 14:17:30 -0400
Subject: [PATCH 1/2] Add full workflow GitHub Action

---
 .github/workflows/full-workflow.yml | 45 +++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 .github/workflows/full-workflow.yml

diff --git a/.github/workflows/full-workflow.yml b/.github/workflows/full-workflow.yml
new file mode 100644
index 0000000..ebdd439
--- /dev/null
+++ b/.github/workflows/full-workflow.yml
@@ -0,0 +1,45 @@
+name: full workflow
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+concurrency:
+  group: full-workflow-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  run-workflow:
+    name: pytest --run-workflow
+    runs-on: ubuntu-latest
+    timeout-minutes: 360
+    permissions:
+      contents: read
+    defaults:
+      run:
+        shell: bash -el {0}
+    env:
+      SNAKEMAKE_CONDA_FRONTEND: mamba
+      GITHUB_PAT: ${{ github.token }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Create test environment
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-file: environment.yml
+          cache-environment: true
+          cache-downloads: true
+
+      - name: Cache Snakemake rule environments
+        uses: actions/cache@v4
+        with:
+          path: .snakemake/conda
+          key: snakemake-conda-full-${{ runner.os }}-${{ hashFiles('workflow/envs/*.yml') }}
+          restore-keys: |
+            snakemake-conda-full-${{ runner.os }}-
+            snakemake-conda-${{ runner.os }}-
+
+      - name: Run full test-data workflow
+        run: pytest tests --run-workflow -q

From 44acbf5dbd06c2ee1c5f2d8e30854dc269de4a04 Mon Sep 17 00:00:00 2001
From: Adam Freedman <adamfreedman@fas.harvard.edu>
Date: Wed, 10 Jun 2026 14:52:46 -0400
Subject: [PATCH 2/2] Set test-data resources for full workflow action

---
 .github/workflows/full-workflow.yml | 37 +++++++++++++++++++++++++++++
 tests/run_test_workflow.sh          |  8 +++++++
 2 files changed, 45 insertions(+)

diff --git a/.github/workflows/full-workflow.yml b/.github/workflows/full-workflow.yml
index ebdd439..a9a7360 100644
--- a/.github/workflows/full-workflow.yml
+++ b/.github/workflows/full-workflow.yml
@@ -21,6 +21,43 @@ jobs:
     env:
       SNAKEMAKE_CONDA_FRONTEND: mamba
       GITHUB_PAT: ${{ github.token }}
+      TEST_WORKFLOW_SNAKEMAKE_ARGS: >-
+        --resources mem_mb=8192
+        --set-resources
+        cellbender:mem_mb=3072
+        cellbender:runtime=30
+        tenx2seuratrds:mem_mb=2048
+        tenx2seuratrds:runtime=10
+        emptydrops:mem_mb=2048
+        emptydrops:runtime=10
+        soupx:mem_mb=2048
+        soupx:runtime=10
+        soupx_emptydrops:mem_mb=2048
+        soupx_emptydrops:runtime=10
+        cellbender2seurat:mem_mb=2048
+        cellbender2seurat:runtime=10
+        doubletfinder:mem_mb=2048
+        doubletfinder:runtime=10
+        doubletfinder_cellbender:mem_mb=2048
+        doubletfinder_cellbender:runtime=10
+        scdblfinder:mem_mb=3072
+        scdblfinder:runtime=10
+        scdblfinder_cellbender:mem_mb=3072
+        scdblfinder_cellbender:runtime=10
+        posthocfilter_mad:mem_mb=3072
+        posthocfilter_mad:runtime=10
+        posthocfilter_mad_cellbender:mem_mb=3072
+        posthocfilter_mad_cellbender:runtime=10
+        posthocfilter_threshold:mem_mb=2048
+        posthocfilter_threshold:runtime=10
+        posthocfilter_threshold_cellbender:mem_mb=2048
+        posthocfilter_threshold_cellbender:runtime=10
+        marker_manifest:mem_mb=1024
+        marker_manifest:runtime=5
+        find_markers:mem_mb=2048
+        find_markers:runtime=5
+        combine_markers:mem_mb=1024
+        combine_markers:runtime=5
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
diff --git a/tests/run_test_workflow.sh b/tests/run_test_workflow.sh
index f3136a4..316a5cc 100755
--- a/tests/run_test_workflow.sh
+++ b/tests/run_test_workflow.sh
@@ -12,6 +12,7 @@ set -euo pipefail
 
 usage() {
     echo "Usage: $0 [--conda-prefix PATH] [additional snakemake args...]"
+    echo "Set TEST_WORKFLOW_SNAKEMAKE_ARGS to append whitespace-delimited Snakemake args before command-line extras."
 }
 
 script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)
@@ -61,6 +62,12 @@ if [[ -n "${snakemake_conda_prefix}" ]]; then
     conda_prefix_args=(--conda-prefix "${snakemake_conda_prefix}")
 fi
 
+env_snakemake_args=()
+if [[ -n "${TEST_WORKFLOW_SNAKEMAKE_ARGS:-}" ]]; then
+    # Intended for simple Snakemake CLI tokens, such as --set-resources entries.
+    read -r -a env_snakemake_args <<< "${TEST_WORKFLOW_SNAKEMAKE_ARGS}"
+fi
+
 snakemake --unlock "${common_args[@]}" "${conda_prefix_args[@]}"
 rm -rf testdata/results
 
@@ -71,4 +78,5 @@ snakemake \
     --retries 2 \
     --jobs 200 \
     --latency-wait 600 \
+    "${env_snakemake_args[@]}" \
     "${extra_snakemake_args[@]}"