CLI Reference

This reference is aligned to the actual Click commands implemented in micos/cli.py.

Invocation pattern

python -m micos.cli [GLOBAL_OPTIONS] <COMMAND> [COMMAND_OPTIONS]

If installed via pyproject.toml, the entrypoint is also available as:

micos [GLOBAL_OPTIONS] <COMMAND> [COMMAND_OPTIONS]

Global options

Option	Description
--config	path to the analysis configuration file
--log-file	optional log output file
--verbose	enable debug logging
--dry-run	print planned work without executing it
--version	print version information

Stable commands

validate-config

Validate the effective configuration before a run.

python -m micos.cli validate-config --config config/analysis.yaml

full-run

Run the end-to-end stable pipeline surface.

python -m micos.cli full-run \
  --input-dir data/raw_input \
  --results-dir results \
  --threads 16 \
  --kneaddata-db /db/kneaddata/human_genome \
  --kraken2-db /db/kraken2/standard

Key flags:

• --skip-qc
• --skip-taxonomy
• --skip-functional
• --skip-diversity

run quality-control

python -m micos.cli run quality-control \
  --input-dir data/raw_input \
  --output-dir results/quality_control \
  --threads 8 \
  --kneaddata-db /db/kneaddata/human_genome

run taxonomic-profiling

python -m micos.cli run taxonomic-profiling \
  --input-dir results/quality_control/kneaddata \
  --output-dir results/taxonomic_profiling \
  --threads 16 \
  --kraken2-db /db/kraken2/standard \
  --confidence 0.1

run diversity-analysis

python -m micos.cli run diversity-analysis \
  --input-biom results/taxonomic_profiling/feature-table.biom \
  --output-dir results/diversity_analysis

run functional-annotation

python -m micos.cli run functional-annotation \
  --input-dir results/quality_control/kneaddata \
  --output-dir results/functional_annotation \
  --threads 8

run summarize-results

python -m micos.cli run summarize-results \
  --results-dir results \
  --output-file results/micos_summary_report.html

Wrapper scripts

Two shell wrappers matter operationally:

Wrapper	Role
scripts/run_full_analysis.sh	thin compatibility layer around micos full-run
scripts/run_module.sh	module wrapper that delegates to stable CLI commands

The important architectural point is that these wrappers delegate. They are not documented here as separate pipeline implementations.

Return codes

The CLI defines explicit exit codes in micos/cli.py:

Code	Meaning
0	success
1	general error
2	invalid arguments
3	configuration error
4	missing dependencies
5	database error
6	I/O error
130	interrupted

Practical note

If you see older examples that imply additional global flags or broader command coverage, prefer this page. It is aligned to the current implemented surface, not to earlier documentation drift.