From c491b33dc76261effb06575c9b4bf585dce52165 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Mon, 26 Jan 2026 04:56:14 +0000
Subject: [PATCH 1/2] Add Snakemake workflow for QA pipelines

Create Snakemake pipelines for orchestrating QA analysis:
- Motion plots: generates traces, FD plots, and violin plots from fMRIprep
- tSNR plots: computes tSNR volumes then generates mosaics and plots
- ISC plots: computes ISC then generates violin and surface plots

Each pipeline properly handles dependencies (tSNR/ISC computation before plotting).
Added snakemake>=8.0.0 as optional 'workflow' dependency.
---
 pyproject.toml              |   3 +
 workflow/README.md          | 119 ++++++++++++++++
 workflow/Snakefile          | 272 ++++++++++++++++++++++++++++++++++++
 workflow/config/config.yaml |  17 +++
 4 files changed, 411 insertions(+)
 create mode 100644 workflow/README.md
 create mode 100644 workflow/Snakefile
 create mode 100644 workflow/config/config.yaml

diff --git a/pyproject.toml b/pyproject.toml
index aaead77..208ea59 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -55,6 +55,9 @@ dev = [
     "pytest>=6.0",
     "ruff>=0.1.0",
 ]
+workflow = [
+    "snakemake>=8.0.0",
+]
 
 [project.urls]
 Homepage = "https://github.com/mvdoc/hyperface-data-paper"
diff --git a/workflow/README.md b/workflow/README.md
new file mode 100644
index 0000000..3708c80
--- /dev/null
+++ b/workflow/README.md
@@ -0,0 +1,119 @@
+# QA Pipeline Workflow
+
+This Snakemake workflow orchestrates the QA analysis pipelines for motion, tSNR, and ISC plots.
+
+## Installation
+
+Install snakemake as an optional dependency:
+
+```bash
+uv sync --extra workflow
+```
+
+Or install snakemake directly:
+
+```bash
+uv pip install snakemake>=8.0.0
+```
+
+## Usage
+
+All commands should be run from the project root directory.
+
+### Run all QA pipelines
+
+```bash
+snakemake --snakefile workflow/Snakefile --cores 1
+```
+
+### Run specific pipelines
+
+```bash
+# Motion plots only
+snakemake --snakefile workflow/Snakefile motion_plots --cores 1
+
+# tSNR plots (includes tSNR computation)
+snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1
+
+# ISC plots (includes ISC computation)
+snakemake --snakefile workflow/Snakefile isc_plots --cores 1
+```
+
+### Dry run (preview what would be executed)
+
+```bash
+snakemake --snakefile workflow/Snakefile -n
+```
+
+### Process specific subjects
+
+```bash
+snakemake --snakefile workflow/Snakefile motion_plots --cores 1 --config subjects="sub-001 sub-002"
+```
+
+### Force regeneration
+
+```bash
+snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1 --forcerun
+```
+
+### Generate HTML reports
+
+```bash
+# Motion HTML reports
+snakemake --snakefile workflow/Snakefile motion_report --cores 1
+
+# tSNR HTML reports
+snakemake --snakefile workflow/Snakefile tsnr_report --cores 1
+```
+
+### Summary statistics
+
+```bash
+snakemake --snakefile workflow/Snakefile tsnr_summary motion_summary --cores 1
+```
+
+## Pipeline Dependencies
+
+```
+fMRIprep outputs
+├── motion_plots ─────────────────────→ motion figures
+│   └── motion_report ────────────────→ HTML reports
+│   └── motion_summary ───────────────→ summary stats
+│
+├── compute_tsnr ─────→ tsnr volumes
+│   └── tsnr_plots ───────────────────→ tsnr figures
+│       └── tsnr_report ──────────────→ HTML reports
+│   └── tsnr_summary ─────────────────→ summary stats
+│
+└── compute_isc ──────→ ISC data
+    └── isc_plots ────────────────────→ ISC figures
+```
+
+## Configuration
+
+Edit `workflow/config/config.yaml` to:
+- Enable/disable specific pipelines
+- Filter subjects to process
+- Force regeneration of outputs
+
+The actual data paths are read from `src/hyperface/assets/qa_config.yaml`.
+
+## Outputs
+
+All outputs are saved under `data/derivatives/qa/`:
+- `motion/` - Motion traces, FD traces, violin plots
+- `tsnr/` - tSNR mosaics, violin plots, surface plots
+- `isc/` - ISC violin plots, surface plots
+
+## Cleanup
+
+```bash
+# Remove specific outputs
+snakemake --snakefile workflow/Snakefile clean_motion
+snakemake --snakefile workflow/Snakefile clean_tsnr
+snakemake --snakefile workflow/Snakefile clean_isc
+
+# Remove all QA outputs
+snakemake --snakefile workflow/Snakefile clean_all
+```
diff --git a/workflow/Snakefile b/workflow/Snakefile
new file mode 100644
index 0000000..fbaa185
--- /dev/null
+++ b/workflow/Snakefile
@@ -0,0 +1,272 @@
+"""Snakemake workflow for QA pipeline plots.
+
+This workflow runs the QA pipeline scripts to generate:
+- Motion plots (directly from fMRIprep confounds)
+- tSNR plots (requires tSNR computation first)
+- ISC plots (requires ISC computation first)
+
+Usage:
+    # Run all QA pipelines
+    snakemake --cores 1
+
+    # Run specific pipeline
+    snakemake motion_plots --cores 1
+    snakemake tsnr_plots --cores 1
+    snakemake isc_plots --cores 1
+
+    # Dry run to see what would be executed
+    snakemake -n
+
+    # Process specific subjects (motion/tsnr only)
+    snakemake motion_plots --cores 1 --config subjects="sub-001 sub-002"
+
+    # Force rerun of specific target
+    snakemake tsnr_plots --cores 1 --forcerun
+"""
+
+import os
+from pathlib import Path
+
+# Configuration
+configfile: "workflow/config/config.yaml"
+
+# Get project root (parent of workflow directory)
+PROJECT_ROOT = Path(workflow.basedir).parent
+
+# Python interpreter from virtual environment
+PYTHON = PROJECT_ROOT / ".venv" / "bin" / "python"
+
+# Scripts directory
+SCRIPTS_DIR = PROJECT_ROOT / "scripts" / "qa"
+
+# Data directories (from qa_config.yaml defaults)
+DATA_DIR = PROJECT_ROOT / "data"
+DERIVATIVES_DIR = DATA_DIR / "derivatives"
+FMRIPREP_DIR = DERIVATIVES_DIR / "fmriprep"
+QA_DIR = DERIVATIVES_DIR / "qa"
+TSNR_DIR = QA_DIR / "tsnr"
+MOTION_DIR = QA_DIR / "motion"
+ISC_DIR = QA_DIR / "isc"
+
+
+def get_subjects_arg():
+    """Get --subjects argument if configured."""
+    subjects = config.get("subjects", "")
+    if subjects:
+        return f"--subjects {subjects}"
+    return ""
+
+
+# Default target: run all QA pipelines
+rule all:
+    input:
+        rules.motion_plots.output if config.get("run_motion", True) else [],
+        rules.tsnr_plots.output if config.get("run_tsnr", True) else [],
+        rules.isc_plots.output if config.get("run_isc", True) else [],
+
+
+# =============================================================================
+# Motion Plots Pipeline
+# =============================================================================
+# Motion plots read directly from fMRIprep confounds files (no pre-computation)
+
+rule motion_plots:
+    """Generate motion QA plots from fMRIprep confounds."""
+    input:
+        script=SCRIPTS_DIR / "qa-plot-motion.py",
+        # Sentinel file to check fMRIprep exists
+        fmriprep=ancient(FMRIPREP_DIR),
+    output:
+        done=touch(MOTION_DIR / ".motion_plots.done"),
+    log:
+        MOTION_DIR / "logs" / "motion_plots.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        mkdir -p {MOTION_DIR}/logs
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+# =============================================================================
+# tSNR Pipeline
+# =============================================================================
+# tSNR plots require pre-computed tSNR volumes
+
+rule compute_tsnr:
+    """Compute tSNR volumes from fMRIprep BOLD data."""
+    input:
+        script=SCRIPTS_DIR / "qa-save-tsnr-volume.py",
+        fmriprep=ancient(FMRIPREP_DIR),
+    output:
+        done=touch(TSNR_DIR / ".tsnr_computed.done"),
+    log:
+        TSNR_DIR / "logs" / "compute_tsnr.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        mkdir -p {TSNR_DIR}/logs
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+rule tsnr_plots:
+    """Generate tSNR QA plots from pre-computed tSNR volumes."""
+    input:
+        script=SCRIPTS_DIR / "qa-plot-tsnr.py",
+        tsnr_computed=TSNR_DIR / ".tsnr_computed.done",
+    output:
+        done=touch(TSNR_DIR / ".tsnr_plots.done"),
+    log:
+        TSNR_DIR / "logs" / "tsnr_plots.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+# =============================================================================
+# ISC Pipeline
+# =============================================================================
+# ISC plots require pre-computed ISC data
+
+rule compute_isc:
+    """Compute inter-subject correlation for visualmemory task."""
+    input:
+        script=SCRIPTS_DIR / "qa-save-isc.py",
+        fmriprep=ancient(FMRIPREP_DIR),
+    output:
+        done=touch(ISC_DIR / ".isc_computed.done"),
+    log:
+        ISC_DIR / "logs" / "compute_isc.log",
+    threads:
+        workflow.cores
+    shell:
+        """
+        mkdir -p {ISC_DIR}/logs
+        {PYTHON} {input.script} --n-jobs {threads} 2>&1 | tee {log}
+        """
+
+
+rule isc_plots:
+    """Generate ISC visualization plots."""
+    input:
+        script=SCRIPTS_DIR / "qa-plot-isc.py",
+        isc_computed=ISC_DIR / ".isc_computed.done",
+    output:
+        done=touch(ISC_DIR / ".isc_plots.done"),
+    log:
+        ISC_DIR / "logs" / "isc_plots.log",
+    shell:
+        """
+        {PYTHON} {input.script} 2>&1 | tee {log}
+        """
+
+
+# =============================================================================
+# HTML Reports (optional, after plots)
+# =============================================================================
+
+rule motion_report:
+    """Generate HTML reports for motion QA."""
+    input:
+        script=SCRIPTS_DIR / "qa-generate-html-reports-motion.py",
+        plots_done=MOTION_DIR / ".motion_plots.done",
+    output:
+        done=touch(MOTION_DIR / ".motion_reports.done"),
+    log:
+        MOTION_DIR / "logs" / "motion_reports.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+rule tsnr_report:
+    """Generate HTML reports for tSNR QA."""
+    input:
+        script=SCRIPTS_DIR / "qa-generate-html-reports-tsnr.py",
+        plots_done=TSNR_DIR / ".tsnr_plots.done",
+    output:
+        done=touch(TSNR_DIR / ".tsnr_reports.done"),
+    log:
+        TSNR_DIR / "logs" / "tsnr_reports.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+# =============================================================================
+# Summary Statistics (optional)
+# =============================================================================
+
+rule tsnr_summary:
+    """Print tSNR summary statistics."""
+    input:
+        script=SCRIPTS_DIR / "print-tsnr-summary.py",
+        tsnr_computed=TSNR_DIR / ".tsnr_computed.done",
+    output:
+        summary=TSNR_DIR / "tsnr_summary.txt",
+    log:
+        TSNR_DIR / "logs" / "tsnr_summary.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+rule motion_summary:
+    """Print motion summary statistics."""
+    input:
+        script=SCRIPTS_DIR / "print-motion-summary.py",
+        fmriprep=ancient(FMRIPREP_DIR),
+    output:
+        summary=MOTION_DIR / "motion_summary.txt",
+    log:
+        MOTION_DIR / "logs" / "motion_summary.log",
+    params:
+        subjects=get_subjects_arg(),
+    shell:
+        """
+        mkdir -p {MOTION_DIR}/logs
+        {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
+        """
+
+
+# =============================================================================
+# Cleanup Rules
+# =============================================================================
+
+rule clean_motion:
+    """Remove motion QA outputs (regenerate with snakemake motion_plots)."""
+    shell:
+        "rm -rf {MOTION_DIR}"
+
+
+rule clean_tsnr:
+    """Remove tSNR QA outputs (regenerate with snakemake tsnr_plots)."""
+    shell:
+        "rm -rf {TSNR_DIR}"
+
+
+rule clean_isc:
+    """Remove ISC QA outputs (regenerate with snakemake isc_plots)."""
+    shell:
+        "rm -rf {ISC_DIR}"
+
+
+rule clean_all:
+    """Remove all QA outputs."""
+    shell:
+        "rm -rf {QA_DIR}"
diff --git a/workflow/config/config.yaml b/workflow/config/config.yaml
new file mode 100644
index 0000000..490ca9f
--- /dev/null
+++ b/workflow/config/config.yaml
@@ -0,0 +1,17 @@
+# Snakemake configuration for QA pipelines
+#
+# This config controls which pipelines run and their parameters.
+# The actual data paths are read from the hyperface QA config
+# (src/hyperface/assets/qa_config.yaml).
+
+# Which pipelines to run with the default 'all' target
+run_motion: true
+run_tsnr: true
+run_isc: true
+
+# Subject filtering (space-separated list, leave empty for all subjects)
+# Example: "sub-001 sub-002 sub-003"
+subjects: ""
+
+# Whether to force regeneration of outputs that already exist
+force: false

From 6b0b120daf3bf16ed489ab1a10d2a1a03082f185 Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Mon, 26 Jan 2026 15:02:20 +0000
Subject: [PATCH 2/2] Fix issues in Snakemake workflow

- Remove unused import (os)
- Fix Python interpreter detection: prefer active interpreter, fallback to .venv
- Fix configfile path using workflow.source_path() for portability
- Add missing log directory creation in tsnr_plots, isc_plots rules
- Add localrules declaration for clean targets (run locally, not on cluster)
- Convert all Path objects to strings for shell commands
- Remove unused 'force' config option
- Remove unnecessary README.md
---
 workflow/README.md          | 119 -------------------------------
 workflow/Snakefile          | 136 ++++++++++++++++++++----------------
 workflow/config/config.yaml |   3 -
 3 files changed, 74 insertions(+), 184 deletions(-)
 delete mode 100644 workflow/README.md

diff --git a/workflow/README.md b/workflow/README.md
deleted file mode 100644
index 3708c80..0000000
--- a/workflow/README.md
+++ /dev/null
@@ -1,119 +0,0 @@
-# QA Pipeline Workflow
-
-This Snakemake workflow orchestrates the QA analysis pipelines for motion, tSNR, and ISC plots.
-
-## Installation
-
-Install snakemake as an optional dependency:
-
-```bash
-uv sync --extra workflow
-```
-
-Or install snakemake directly:
-
-```bash
-uv pip install snakemake>=8.0.0
-```
-
-## Usage
-
-All commands should be run from the project root directory.
-
-### Run all QA pipelines
-
-```bash
-snakemake --snakefile workflow/Snakefile --cores 1
-```
-
-### Run specific pipelines
-
-```bash
-# Motion plots only
-snakemake --snakefile workflow/Snakefile motion_plots --cores 1
-
-# tSNR plots (includes tSNR computation)
-snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1
-
-# ISC plots (includes ISC computation)
-snakemake --snakefile workflow/Snakefile isc_plots --cores 1
-```
-
-### Dry run (preview what would be executed)
-
-```bash
-snakemake --snakefile workflow/Snakefile -n
-```
-
-### Process specific subjects
-
-```bash
-snakemake --snakefile workflow/Snakefile motion_plots --cores 1 --config subjects="sub-001 sub-002"
-```
-
-### Force regeneration
-
-```bash
-snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1 --forcerun
-```
-
-### Generate HTML reports
-
-```bash
-# Motion HTML reports
-snakemake --snakefile workflow/Snakefile motion_report --cores 1
-
-# tSNR HTML reports
-snakemake --snakefile workflow/Snakefile tsnr_report --cores 1
-```
-
-### Summary statistics
-
-```bash
-snakemake --snakefile workflow/Snakefile tsnr_summary motion_summary --cores 1
-```
-
-## Pipeline Dependencies
-
-```
-fMRIprep outputs
-├── motion_plots ─────────────────────→ motion figures
-│   └── motion_report ────────────────→ HTML reports
-│   └── motion_summary ───────────────→ summary stats
-│
-├── compute_tsnr ─────→ tsnr volumes
-│   └── tsnr_plots ───────────────────→ tsnr figures
-│       └── tsnr_report ──────────────→ HTML reports
-│   └── tsnr_summary ─────────────────→ summary stats
-│
-└── compute_isc ──────→ ISC data
-    └── isc_plots ────────────────────→ ISC figures
-```
-
-## Configuration
-
-Edit `workflow/config/config.yaml` to:
-- Enable/disable specific pipelines
-- Filter subjects to process
-- Force regeneration of outputs
-
-The actual data paths are read from `src/hyperface/assets/qa_config.yaml`.
-
-## Outputs
-
-All outputs are saved under `data/derivatives/qa/`:
-- `motion/` - Motion traces, FD traces, violin plots
-- `tsnr/` - tSNR mosaics, violin plots, surface plots
-- `isc/` - ISC violin plots, surface plots
-
-## Cleanup
-
-```bash
-# Remove specific outputs
-snakemake --snakefile workflow/Snakefile clean_motion
-snakemake --snakefile workflow/Snakefile clean_tsnr
-snakemake --snakefile workflow/Snakefile clean_isc
-
-# Remove all QA outputs
-snakemake --snakefile workflow/Snakefile clean_all
-```
diff --git a/workflow/Snakefile b/workflow/Snakefile
index fbaa185..c21e550 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -6,47 +6,55 @@ This workflow runs the QA pipeline scripts to generate:
 - ISC plots (requires ISC computation first)
 
 Usage:
-    # Run all QA pipelines
-    snakemake --cores 1
+    # Run all QA pipelines (from project root)
+    snakemake --snakefile workflow/Snakefile --cores 1
 
     # Run specific pipeline
-    snakemake motion_plots --cores 1
-    snakemake tsnr_plots --cores 1
-    snakemake isc_plots --cores 1
+    snakemake --snakefile workflow/Snakefile motion_plots --cores 1
+    snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1
+    snakemake --snakefile workflow/Snakefile isc_plots --cores 1
 
     # Dry run to see what would be executed
-    snakemake -n
+    snakemake --snakefile workflow/Snakefile -n
 
     # Process specific subjects (motion/tsnr only)
-    snakemake motion_plots --cores 1 --config subjects="sub-001 sub-002"
+    snakemake --snakefile workflow/Snakefile motion_plots --cores 1 --config subjects="sub-001 sub-002"
 
     # Force rerun of specific target
-    snakemake tsnr_plots --cores 1 --forcerun
+    snakemake --snakefile workflow/Snakefile tsnr_plots --cores 1 --forcerun
 """
 
-import os
+import shutil
+import sys
 from pathlib import Path
 
-# Configuration
-configfile: "workflow/config/config.yaml"
-
 # Get project root (parent of workflow directory)
 PROJECT_ROOT = Path(workflow.basedir).parent
 
-# Python interpreter from virtual environment
-PYTHON = PROJECT_ROOT / ".venv" / "bin" / "python"
+# Configuration - use path relative to workflow directory
+configfile: workflow.source_path("config/config.yaml")
+
+# Python interpreter - prefer active interpreter, fallback to venv
+VENV_PYTHON = PROJECT_ROOT / ".venv" / "bin" / "python"
+if Path(sys.executable).is_file():
+    PYTHON = str(sys.executable)
+elif VENV_PYTHON.is_file():
+    PYTHON = str(VENV_PYTHON)
+else:
+    # Fallback to system python
+    PYTHON = shutil.which("python3") or shutil.which("python") or "python"
 
 # Scripts directory
-SCRIPTS_DIR = PROJECT_ROOT / "scripts" / "qa"
+SCRIPTS_DIR = str(PROJECT_ROOT / "scripts" / "qa")
 
 # Data directories (from qa_config.yaml defaults)
-DATA_DIR = PROJECT_ROOT / "data"
-DERIVATIVES_DIR = DATA_DIR / "derivatives"
-FMRIPREP_DIR = DERIVATIVES_DIR / "fmriprep"
-QA_DIR = DERIVATIVES_DIR / "qa"
-TSNR_DIR = QA_DIR / "tsnr"
-MOTION_DIR = QA_DIR / "motion"
-ISC_DIR = QA_DIR / "isc"
+DATA_DIR = str(PROJECT_ROOT / "data")
+DERIVATIVES_DIR = f"{DATA_DIR}/derivatives"
+FMRIPREP_DIR = f"{DERIVATIVES_DIR}/fmriprep"
+QA_DIR = f"{DERIVATIVES_DIR}/qa"
+TSNR_DIR = f"{QA_DIR}/tsnr"
+MOTION_DIR = f"{QA_DIR}/motion"
+ISC_DIR = f"{QA_DIR}/isc"
 
 
 def get_subjects_arg():
@@ -57,12 +65,16 @@ def get_subjects_arg():
     return ""
 
 
+# Declare rules that don't create output files (run locally, not on cluster)
+localrules: all, clean_motion, clean_tsnr, clean_isc, clean_all
+
+
 # Default target: run all QA pipelines
 rule all:
     input:
-        rules.motion_plots.output if config.get("run_motion", True) else [],
-        rules.tsnr_plots.output if config.get("run_tsnr", True) else [],
-        rules.isc_plots.output if config.get("run_isc", True) else [],
+        f"{MOTION_DIR}/.motion_plots.done" if config.get("run_motion", True) else [],
+        f"{TSNR_DIR}/.tsnr_plots.done" if config.get("run_tsnr", True) else [],
+        f"{ISC_DIR}/.isc_plots.done" if config.get("run_isc", True) else [],
 
 
 # =============================================================================
@@ -73,13 +85,11 @@ rule all:
 rule motion_plots:
     """Generate motion QA plots from fMRIprep confounds."""
     input:
-        script=SCRIPTS_DIR / "qa-plot-motion.py",
-        # Sentinel file to check fMRIprep exists
-        fmriprep=ancient(FMRIPREP_DIR),
+        script=f"{SCRIPTS_DIR}/qa-plot-motion.py",
     output:
-        done=touch(MOTION_DIR / ".motion_plots.done"),
+        done=touch(f"{MOTION_DIR}/.motion_plots.done"),
     log:
-        MOTION_DIR / "logs" / "motion_plots.log",
+        f"{MOTION_DIR}/logs/motion_plots.log",
     params:
         subjects=get_subjects_arg(),
     shell:
@@ -97,12 +107,11 @@ rule motion_plots:
 rule compute_tsnr:
     """Compute tSNR volumes from fMRIprep BOLD data."""
     input:
-        script=SCRIPTS_DIR / "qa-save-tsnr-volume.py",
-        fmriprep=ancient(FMRIPREP_DIR),
+        script=f"{SCRIPTS_DIR}/qa-save-tsnr-volume.py",
     output:
-        done=touch(TSNR_DIR / ".tsnr_computed.done"),
+        done=touch(f"{TSNR_DIR}/.tsnr_computed.done"),
     log:
-        TSNR_DIR / "logs" / "compute_tsnr.log",
+        f"{TSNR_DIR}/logs/compute_tsnr.log",
     params:
         subjects=get_subjects_arg(),
     shell:
@@ -115,16 +124,17 @@ rule compute_tsnr:
 rule tsnr_plots:
     """Generate tSNR QA plots from pre-computed tSNR volumes."""
     input:
-        script=SCRIPTS_DIR / "qa-plot-tsnr.py",
-        tsnr_computed=TSNR_DIR / ".tsnr_computed.done",
+        script=f"{SCRIPTS_DIR}/qa-plot-tsnr.py",
+        tsnr_computed=f"{TSNR_DIR}/.tsnr_computed.done",
     output:
-        done=touch(TSNR_DIR / ".tsnr_plots.done"),
+        done=touch(f"{TSNR_DIR}/.tsnr_plots.done"),
     log:
-        TSNR_DIR / "logs" / "tsnr_plots.log",
+        f"{TSNR_DIR}/logs/tsnr_plots.log",
     params:
         subjects=get_subjects_arg(),
     shell:
         """
+        mkdir -p {TSNR_DIR}/logs
         {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
         """
 
@@ -137,12 +147,11 @@ rule tsnr_plots:
 rule compute_isc:
     """Compute inter-subject correlation for visualmemory task."""
     input:
-        script=SCRIPTS_DIR / "qa-save-isc.py",
-        fmriprep=ancient(FMRIPREP_DIR),
+        script=f"{SCRIPTS_DIR}/qa-save-isc.py",
     output:
-        done=touch(ISC_DIR / ".isc_computed.done"),
+        done=touch(f"{ISC_DIR}/.isc_computed.done"),
     log:
-        ISC_DIR / "logs" / "compute_isc.log",
+        f"{ISC_DIR}/logs/compute_isc.log",
     threads:
         workflow.cores
     shell:
@@ -155,14 +164,15 @@ rule compute_isc:
 rule isc_plots:
     """Generate ISC visualization plots."""
     input:
-        script=SCRIPTS_DIR / "qa-plot-isc.py",
-        isc_computed=ISC_DIR / ".isc_computed.done",
+        script=f"{SCRIPTS_DIR}/qa-plot-isc.py",
+        isc_computed=f"{ISC_DIR}/.isc_computed.done",
     output:
-        done=touch(ISC_DIR / ".isc_plots.done"),
+        done=touch(f"{ISC_DIR}/.isc_plots.done"),
     log:
-        ISC_DIR / "logs" / "isc_plots.log",
+        f"{ISC_DIR}/logs/isc_plots.log",
     shell:
         """
+        mkdir -p {ISC_DIR}/logs
         {PYTHON} {input.script} 2>&1 | tee {log}
         """
 
@@ -174,16 +184,17 @@ rule isc_plots:
 rule motion_report:
     """Generate HTML reports for motion QA."""
     input:
-        script=SCRIPTS_DIR / "qa-generate-html-reports-motion.py",
-        plots_done=MOTION_DIR / ".motion_plots.done",
+        script=f"{SCRIPTS_DIR}/qa-generate-html-reports-motion.py",
+        plots_done=f"{MOTION_DIR}/.motion_plots.done",
     output:
-        done=touch(MOTION_DIR / ".motion_reports.done"),
+        done=touch(f"{MOTION_DIR}/.motion_reports.done"),
     log:
-        MOTION_DIR / "logs" / "motion_reports.log",
+        f"{MOTION_DIR}/logs/motion_reports.log",
     params:
         subjects=get_subjects_arg(),
     shell:
         """
+        mkdir -p {MOTION_DIR}/logs
         {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
         """
 
@@ -191,16 +202,17 @@ rule motion_report:
 rule tsnr_report:
     """Generate HTML reports for tSNR QA."""
     input:
-        script=SCRIPTS_DIR / "qa-generate-html-reports-tsnr.py",
-        plots_done=TSNR_DIR / ".tsnr_plots.done",
+        script=f"{SCRIPTS_DIR}/qa-generate-html-reports-tsnr.py",
+        plots_done=f"{TSNR_DIR}/.tsnr_plots.done",
     output:
-        done=touch(TSNR_DIR / ".tsnr_reports.done"),
+        done=touch(f"{TSNR_DIR}/.tsnr_reports.done"),
     log:
-        TSNR_DIR / "logs" / "tsnr_reports.log",
+        f"{TSNR_DIR}/logs/tsnr_reports.log",
     params:
         subjects=get_subjects_arg(),
     shell:
         """
+        mkdir -p {TSNR_DIR}/logs
         {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
         """
 
@@ -212,16 +224,17 @@ rule tsnr_report:
 rule tsnr_summary:
     """Print tSNR summary statistics."""
     input:
-        script=SCRIPTS_DIR / "print-tsnr-summary.py",
-        tsnr_computed=TSNR_DIR / ".tsnr_computed.done",
+        script=f"{SCRIPTS_DIR}/print-tsnr-summary.py",
+        tsnr_computed=f"{TSNR_DIR}/.tsnr_computed.done",
     output:
-        summary=TSNR_DIR / "tsnr_summary.txt",
+        summary=f"{TSNR_DIR}/tsnr_summary.txt",
     log:
-        TSNR_DIR / "logs" / "tsnr_summary.log",
+        f"{TSNR_DIR}/logs/tsnr_summary.log",
     params:
         subjects=get_subjects_arg(),
     shell:
         """
+        mkdir -p {TSNR_DIR}/logs
         {PYTHON} {input.script} {params.subjects} 2>&1 | tee {log}
         """
 
@@ -229,12 +242,11 @@ rule tsnr_summary:
 rule motion_summary:
     """Print motion summary statistics."""
     input:
-        script=SCRIPTS_DIR / "print-motion-summary.py",
-        fmriprep=ancient(FMRIPREP_DIR),
+        script=f"{SCRIPTS_DIR}/print-motion-summary.py",
     output:
-        summary=MOTION_DIR / "motion_summary.txt",
+        summary=f"{MOTION_DIR}/motion_summary.txt",
     log:
-        MOTION_DIR / "logs" / "motion_summary.log",
+        f"{MOTION_DIR}/logs/motion_summary.log",
     params:
         subjects=get_subjects_arg(),
     shell:
diff --git a/workflow/config/config.yaml b/workflow/config/config.yaml
index 490ca9f..9c2ca99 100644
--- a/workflow/config/config.yaml
+++ b/workflow/config/config.yaml
@@ -12,6 +12,3 @@ run_isc: true
 # Subject filtering (space-separated list, leave empty for all subjects)
 # Example: "sub-001 sub-002 sub-003"
 subjects: ""
-
-# Whether to force regeneration of outputs that already exist
-force: false