minimap2-align

name	minimap2-align
description	Runs project-specific minimap2 splice-aware alignment for long-read RNA-seq, primarily for ONT single-cell reads after BLAZE, with explicit preset selection, tag-preservation handling, and command confirmation.

minimap2 Align

Use this skill for the genome-alignment step in the project workflow.

Primary skill file:

• ./SKILL.md

Use This Skill When

• long-read RNA reads need splice-aware genome alignment
• downstream processing requires SAM or BAM
• ONT BLAZE-demultiplexed reads need mapping to the genome

Mandatory Rules

1. Use the minimap2 conda environment for this skill's commands.
2. Ask minimap2-specific questions only when the workflow reaches this step.
3. Confirm the alignment preset explicitly, typically:
   • -x splice for ONT
   • -x splice:hq for PacBio CCS if alignment is explicitly requested
4. Confirm thread count explicitly.
5. If BLAZE wrote CB:Z and UB:Z tags into FASTQ comments, preserve them with -y.
6. Derive output SAM under the workflow-level results root.
7. Run the minimap2 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 minimap2.
9. Before execution, show the exact minimap2 command, the planned tmux session name, and wait for confirmation.
10. After launch, do not exit that tmux session until the minimap2 command has finished.
11. Execute the confirmed minimap2 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 minimap2 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 02_minimap2 as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.

Default Project Guidance

• ONT standard route: minimap2 -ax splice -y -t <threads> ref.fa reads.fastq.gz > aln.sam
• Do not surface low-level scoring and indexing options unless needed.