blaze-demultiplex

name	blaze-demultiplex
description	Runs project-specific BLAZE demultiplexing for ONT long-read single-cell RNA-seq, including barcode and UMI detection, whitelist generation, chemistry confirmation, and demultiplexed FASTQ production.

BLAZE Demultiplex

Use this skill for the ONT barcode and UMI preprocessing step.

Primary skill file:

• ./SKILL.md

Use This Skill When

• the platform is ONT
• input is raw long-read FASTQ or FASTQ.gz
• barcode and UMI calling are still needed
• a whitelist and demultiplexed FASTQ are required for downstream steps

Mandatory Rules

1. Use the blaze conda environment for this skill's commands.
2. Do not use this for PacBio direct-quantification runs.
3. Do not silently rely on BLAZE default chemistry.
4. Confirm one chemistry route explicitly:
   • --kit-version
   • or custom barcode route with --full-bc-whitelist and --umi-len
5. Confirm one whitelist-generation mode explicitly unless running demux-only mode.
6. Derive output paths under the workflow-level results root.
7. Run the BLAZE command inside a persistent tmux session.
8. If the session is entered with conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then conda activate blaze.
9. Before execution, show the exact BLAZE command, the planned tmux session name, and wait for confirmation.
10. After launch, do not exit that tmux session until the BLAZE command has finished.
11. Execute the confirmed BLAZE command directly in the shell or in tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.
12. Resolve the BLAZE output subdirectory automatically from the already confirmed workflow-level results root and ask the user to confirm the resolved path rather than asking for a new output directory.
13. Use 01_blaze as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.

Key Decisions To Ask

• chemistry route
• whitelist mode
• thread count
• whether to reuse or overwrite existing outputs

Do not surface low-level tuning unless the user asks or troubleshooting requires it.