samtools-bam-processing

name	samtools-bam-processing
description	Runs project-specific samtools sorting, indexing, quick structural validation, and optional flagstat summary to prepare long-read RNA alignments for downstream quantification.

samtools BAM Processing

Use this skill after alignment output exists and downstream tools require a sorted and indexed BAM.

Primary skill file:

• ./SKILL.md

Use This Skill When

• minimap2 or another aligner has produced SAM or unsorted BAM
• downstream quantification expects sorted and indexed BAM
• minimal BAM integrity checks or a flagstat summary are needed

Mandatory Rules

1. Use the samtools conda environment for this skill's commands.
2. Ask samtools-specific questions only when this step is reached.
3. Prefer samtools sort directly on aligner output unless the user explicitly wants intermediate BAMs.
4. Confirm thread count for sorting explicitly.
5. Derive sorted BAM, index, and optional QC outputs under the workflow-level results root.
6. Run the samtools command block inside a persistent tmux session.
7. If the session is entered with conda activate, first run source "$(conda info --base)/etc/profile.d/conda.sh" inside tmux, then conda activate samtools.
8. If using a coupled block such as sort plus index, show the full command block and the planned tmux session name before execution.
9. Wait for user confirmation before running any samtools command.
10. After launch, do not exit that tmux session until the samtools command block has finished.
11. Execute the confirmed samtools command block directly in the shell or in tmux; do not generate a temporary .sh wrapper unless the user explicitly asks for one.
12. Resolve the samtools 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 03_samtools as the default subdirectory name under the confirmed workflow-level results root unless the user explicitly asks for a different name.

Standard Pattern

samtools sort -@ <threads> -o sample.sorted.bam sample.sam
samtools index sample.sorted.bam