feat: add --output-dir, --skip-plots, and summary.tsv for pipeline integration#31
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…ine use Add three features for batch/pipeline integration (e.g., Nextflow): 1. --output-dir: Explicit output directory that overrides the auto-generated path (folder-outputs/run_name/params). When set, all outputs go to the specified directory with deterministic paths. The auto-generated path remains the default for interactive use. 2. --skip-plots: Skip generating heatmap and logo SVG plots in the consensus step. Plots use matplotlib/seaborn/logomaker which is slow and unnecessary for headless pipeline execution. Available on both `instanexus` (main CLI) and `python -m instanexus.consensus` (module CLI). 3. summary.tsv: A stable summary file written to the experiment output directory at the end of the pipeline. Contains run metadata, paths, and consensus statistics in a single TSV for easy downstream parsing. All 2 existing tests pass. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
The V2 handler clean_winnow_rescored() already checks multiple column name candidates, but main() only checked 'preds' and 'prediction_untokenised'. Winnow outputs use 'prediction', which was missed. Unified the column detection to match the V2 candidates list. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
Add three features to make InstaNexus suitable for automated pipeline execution (e.g., Nextflow/INFlow):
1.
--output-dir— Deterministic output pathsWhen set, all outputs go to the specified directory instead of the auto-generated
folder-outputs/run_name/assembly_mode_params/path. The auto-generated path remains the default for interactive use.2.
--skip-plots— Headless executionSkip generating heatmap (seaborn) and logo (logomaker) SVG plots in the consensus step. These are slow and unnecessary for pipeline execution. Available on both the main
instanexusCLI and thepython -m instanexus.consensusmodule CLI.3.
summary.tsv— Stable summary fileWritten to the experiment output directory at the end of the pipeline. Contains run metadata, output paths, and consensus statistics in a single TSV for easy downstream parsing by pipeline orchestrators.
Motivation
The INFlow pipeline (nf-core/denovoproteomics) wraps InstaNexus as separate Nextflow processes. It needs:
Test plan
instanexus --helpshows new flags🤖 Generated with Claude Code