bambu-quantification

name	bambu-quantification
description	Runs project-specific bambu single-cell transcript discovery and quantification for ONT aligned-BAM input or PacBio raw FASTQ input, with explicit run organization, chemistry handling, and command confirmation.

bambu Quantification

Use this skill when the selected Step 4 tool is bambu.

Primary skill file:

• ./SKILL.md

Use This Skill When

• the user selected bambu
• transcript discovery and transcript or gene count matrices are needed
• ONT input is a demultiplexed and aligned BAM
• or PacBio input is raw FASTQ in direct single-cell mode

Mandatory Rules

1. Ask bambu-specific questions only when the workflow reaches the bambu step.
2. First ask how samples should be organized:
   • one sample per run
   • or multi-sample joint run
3. If the user provides multiple samples or multiple sample-specific input files, explicitly remind them that they should choose the multi-sample joint run.
4. Confirm the correct input route explicitly:
   • --bams for ONT aligned-BAM route
   • --reads for direct raw-read route
5. For PacBio direct runs, confirm chemistry explicitly.
6. Confirm thread count explicitly.
7. Derive --outdir under the workflow-level results root.
8. Run the final Nextflow command or command block inside a persistent tmux session.
9. If the session is entered with conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then activate the bambu runtime environment before launching the final workflow command.
10. Before execution, show the exact final Nextflow command or command block, the planned tmux session name, and wait for confirmation.
11. After launch, do not exit that tmux session until the bambu workflow command has finished.
12. Execute the confirmed bambu workflow command directly in the shell or in tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.
13. Resolve the bambu 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.
14. Use 04_bambu as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.

Runtime Notes

• This project assumes bambu runs through Nextflow.
• Container runtime details are operational, not biological decisions, and should not be surfaced unless needed.