# CoverM

## Purpose
Calculate contig or genome abundance from read mappings.

## When to Use
Use after reads are mapped to plasmid contigs.

## Inputs
`bam`, `plasmid_contigs`, `threads`, `output_dir`.

- Registry inputs: `bam`.
- Template parameters: `bam, abundance, threads`.
- AutoPlasm merges sample fields, step params, and step outputs before rendering the command.

## Outputs
Coverage and abundance table.

- Registry outputs: `output_dir, tool-specific result files`.
- Step stdout/stderr from real execution are captured under `provenance/step_logs/`.

## Environment
- Environment file: `envs/abundance.yml` when present.
- Runtime environment: `autoplasm-abundance`.
- Executable: `coverm`.
- The CLI resolves the executable from `.mamba/envs/{env_name}/bin`; do not depend on a global conda/mamba environment.

## Command Template
`coverm contig --bam-files {bam} --output-file {abundance} --threads {threads}`

## Auto-selection Rules
- Registry state: `default-enabled`, `recommended`.
Default abundance calculator.

## Interactive Parameters
Minimum covered fraction, mapping quality, normalization mode.
- In current CLI behavior, `interactive` is recorded as mode; agents should surface choices to users before writing config values.

## Failure Handling
- Run `autoplasm dry-run` first and inspect `provenance/commands.tsv`.
- For real execution, ensure these rendered parameters are non-empty and not placeholders: `bam`.
Fail early if mapping indexes, BAM files, or read inputs are missing for the selected command template.
- On failure, inspect `provenance/commands.tsv` and the matching `provenance/step_logs/{step_id}.stderr.log`.

## Normalization
Normalize abundance outputs toward raw counts, coverage, RPKM, and TPM tables as configured.

## Agent Usage Notes
- Prefer editing config files or sample sheets, then run `autoplasm plan` and `autoplasm dry-run` before real execution.
- Do not hand-run this command outside AutoPlasm unless debugging a single failed step; preserve provenance through the CLI whenever possible.
- Do not claim biological completion from dry-run output; it only validates planning and command rendering.

## Example
`autoplasm dry-run --config examples/config_minimal.yaml`
