feat: consolidate demux env into default and add edx concordance

Remove the separate `demux` pixi environment by merging WarpDemuX
dependencies into the default env and unified setup script. Rename
warpdemux.smk to demux.smk and add edx_concordance rule for
cross-checking WDX barcode assignment vs 3' EDX adapter identity.
Update all docs and config to reflect the simplified workflow.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jayhesselberth

CLAUDE.md

@@ -159,7 +159,7 @@ The pipeline supports optional barcode demultiplexing using WarpDemuX for pooled
 
 ### Enabling Demultiplexing
 
-1. **Install demux environment**: `pixi install -e demux && pixi run -e demux install-warpdemux`
+1. **Install WarpDemuX**: `pixi run setup` (installs WarpDemuX along with other tools)
 2. **Create YAML sample file** with barcode assignments (see `config/samples-demux-example.yml`)
 3. **Enable in config**: Set `warpdemux.enabled: true`
 
@@ -185,10 +185,10 @@ runs:
 
 ```bash
 # Dry run with demux config
-pixi run -e demux snakemake -n --configfile=config/config-demux-test.yml
+pixi run snakemake -n --configfile=config/config-demux-test.yml
 
 # Execute with demux
-pixi run -e demux snakemake --configfile=config/config-demux-test.yml --cores 8
+pixi run snakemake --configfile=config/config-demux-test.yml --cores 8
 ```
 
 ## Charged vs Uncharged Classification

cluster/slurm/config.yaml

@@ -18,7 +18,7 @@ slurm-delete-logfiles-older-than: 10  # Days
 # Default resources for all rules
 default-resources:
   slurm_partition: "normal"       # Default CPU partition (customize for your cluster)
-  # slurm_account: "aatrnaseq"   # SLURM account/allocation (customize for your cluster)
+  slurm_account: "gpu_rbi"       # SLURM account/allocation (customize for your cluster)
   runtime: 120                 # Default walltime in minutes (2 hours)
   mem_mb: 8000                 # Default memory in MB (8GB)
   cpus_per_task: 1             # Default CPUs per task

config/README.md

@@ -69,7 +69,7 @@ warpdemux:
 Run with the demux environment:
 
 ```bash
-pixi run -e demux snakemake --configfile=config/config-demux.yml --cores 8
+pixi run snakemake --configfile=config/config-demux.yml --cores 8
 ```
 
 See `config-demux-test.yml` for a complete example.

config/config-demux-test.yml

@@ -1,7 +1,7 @@
 # Test config for WarpDemuX demultiplexing
 #
 # This config enables WarpDemuX barcode demultiplexing.
-# Use with: pixi run -e demux snakemake -n --configfile=config/config-demux-test.yml
+# Use with: pixi run snakemake -n --configfile=config/config-demux-test.yml
 
 # Sample file in YAML format with barcode assignments
 samples: config/samples-demux-test.yml

docs/troubleshooting/common-errors.md

@@ -352,10 +352,10 @@ warpdemux: command not found
 
 **Solution:**
 
-Install the demux environment (WarpDemuX is auto-installed on first use):
+Install WarpDemuX via the setup command:
 
 ```bash
-pixi install -e demux
+pixi run setup
 ```
 
 ### Invalid Barcode Kit

docs/user-guide/running-pipeline.md

@@ -241,14 +241,14 @@ pixi run snakemake --report report.html --configfile=config/config.yml
 
 ## With Demultiplexing
 
-For demultiplexed samples, use the `demux` environment:
+For demultiplexed samples, ensure WarpDemuX is installed (`pixi run setup`), then run as usual:
 
 ```bash
 # Dry run
-pixi run -e demux snakemake -n --configfile=config/config-demux.yml
+pixi run snakemake -n --configfile=config/config-demux.yml
 
 # Execute
-pixi run -e demux snakemake --profile cluster/lsf \
+pixi run snakemake --profile cluster/lsf \
     --configfile=config/config-demux.yml
 ```
 

docs/workflow/demultiplexing.md

@@ -31,13 +31,13 @@ Do **not** use when:
 
 ## Setup
 
-### 1. Install Demux Environment
+### 1. Install WarpDemuX
 
 ```bash
-pixi install -e demux
+pixi run setup
 ```
 
-This installs the demux environment dependencies. WarpDemuX itself is automatically installed on first use via the environment activation script.
+This installs WarpDemuX along with other pipeline tools (dorado, remora).
 
 ### 2. Create YAML Sample File
 
@@ -213,17 +213,17 @@ Filters raw POD5 files by sample using read ID list.
 ### Dry Run
 
 ```bash
-pixi run -e demux snakemake -n --configfile=config/config-demux.yml
+pixi run snakemake -n --configfile=config/config-demux.yml
 ```
 
 ### Execute
 
 ```bash
 # Local
-pixi run -e demux snakemake --cores 12 --configfile=config/config-demux.yml
+pixi run snakemake --cores 12 --configfile=config/config-demux.yml
 
 # Cluster
-pixi run -e demux snakemake --profile cluster/lsf --configfile=config/config-demux.yml
+pixi run snakemake --profile cluster/lsf --configfile=config/config-demux.yml
 ```
 
 ## Output Structure
@@ -299,7 +299,7 @@ If barcode distribution is very unbalanced:
 
 1. **Verify barcode distribution** before running full pipeline:
    ```bash
-   pixi run -e demux snakemake demux/read_ids/{run_id}/demux_summary.tsv.gz \
+   pixi run snakemake demux/read_ids/{run_id}/demux_summary.tsv.gz \
        --configfile=config/config-demux.yml
    ```
 

pixi.lock

@@ -33,12 +33,20 @@ ont-modkit = "*"
 ruff = "*"
 yamllint = "*"
 nvitop = ">=1.6.2,<2"
+# WarpDemuX dependencies (compiled packages best from conda)
+dtaidistance = "*"
+scikit-learn = "*"
+scipy = "*"
+cython = "*"
+catboost = "*"
+ruptures = "*"
+bottleneck = "*"
 
 [activation]
 scripts = ["scripts/setup-env.sh"]
 
 [tasks]
-setup = { cmd = "bash scripts/setup-tools.sh && pixi run -e demux install-warpdemux", description = "One-time setup: install dorado, models, remora, and WarpDemuX" }
+setup = { cmd = "bash scripts/setup-tools.sh", description = "One-time setup: install dorado, models, remora, and WarpDemuX" }
 dl-test-data = { cmd = "cd .tests && bash dl_test_data.sh", description = "Download test data" }
 # Pipeline execution
 dry-run = { cmd = "snakemake -n --configfile=config/config-test.yml", description = "Dry run with test config" }
@@ -54,6 +62,9 @@ collapse-ref = { cmd = "python workflow/scripts/collapse_gtrndb_fasta.py", descr
 lint-snakefmt = { cmd = "snakefmt --check workflow/", description = "Check Snakemake formatting" }
 lint-python = { cmd = "ruff check workflow/scripts/ && ruff format --check workflow/scripts/", description = "Lint and check Python formatting" }
 lint-yaml = { cmd = "yamllint -d \"{extends: default, rules: {line-length: {max: 120}, document-start: disable}}\" config/ .github/", description = "Lint YAML files" }
+# WarpDemuX tasks
+install-warpdemux = { cmd = "bash -c '[ -d resources/tools/WarpDemuX ] || git clone --recursive https://github.com/KleistLab/WarpDemuX.git resources/tools/WarpDemuX' && uv pip install -e resources/tools/WarpDemuX", description = "Clone and install WarpDemuX" }
+dry-run-demux = { cmd = "snakemake -n --configfile=config/config-demux-test.yml", description = "Dry run demux test" }
 
 # Testing feature
 [feature.test]
@@ -70,33 +81,6 @@ test-unit = { cmd = "pytest tests/unit/ -v --cov=workflow/scripts", description
 test-integration = { cmd = "pytest tests/integration/ -v", description = "Run integration tests" }
 test-all = { cmd = "pytest tests/ -v --cov=workflow/scripts", description = "Run all tests with coverage" }
 
-# WarpDemuX demultiplexing feature
-[feature.demux]
-platforms = ["linux-64"]
-
-[feature.demux.activation]
-scripts = ["scripts/demux-activate.sh"]
-
-[feature.demux.dependencies]
-# WarpDemuX dependencies
-libstdcxx-ng = ">=12"
-pytorch = "*"
-dtaidistance = "*"
-scikit-learn = "*"
-scipy = "*"
-cython = "*"
-toml = "*"
-tqdm = "*"
-numpy = "<2"
-joblib = "*"
-bottleneck = "*"
-ruptures = "*"
-catboost = "*"
-
-[feature.demux.tasks]
-install-warpdemux = { cmd = "bash -c '[ -d resources/tools/WarpDemuX ] || git clone --recursive https://github.com/KleistLab/WarpDemuX.git resources/tools/WarpDemuX' && uv pip install -e resources/tools/WarpDemuX", description = "Clone and install WarpDemuX" }
-dry-run-demux = { cmd = "snakemake -n --configfile=config/config-demux-test.yml", description = "Dry run demux test" }
-
 # QC Report rendering feature
 [feature.report]
 platforms = ["linux-64"]
@@ -126,5 +110,4 @@ render-qc = { cmd = "snakemake render_all_qc_reports --configfile=config/config-
 [environments]
 default = []
 test = ["test"]
-demux = ["demux"]
 report = ["report"]