{"label": "Lyso-IP QC Pipeline", "stages": [{"params": {"format": "generic_tidy", "raw_file": "/mnt/d/GoLandProjects/cauldronGO/build/bin/linux-amd64/plugins/lysoip-ingestion/examples/generic_tidy_data.csv", "peptide_file": "/mnt/d/GoLandProjects/cauldronGO/build/bin/linux-amd64/plugins/lysoip-ingestion/examples/generic_tidy_peptides.csv", "sample_sheet_file": "/mnt/d/GoLandProjects/cauldronGO/build/bin/linux-amd64/plugins/lysoip-ingestion/examples/sample_sheet.csv"}, "bindings": {}, "pluginId": "lysoip-ingestion", "repository": "https://github.com/noatgnu/lysoip-ingestion-plugin", "requirements": {"python": ">=3.11", "packages": ["pandas>=2.0.0"]}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"samples_file": {"stage": 0, "output": "samples"}, "abundance_long_file": {"stage": 0, "output": "abundance_long"}, "peptide_abundance_file": {"stage": 0, "output": "peptide_abundance_long"}}, "pluginId": "lysoip-differential-expression", "repository": "https://github.com/noatgnu/lysoip-differential-expression-plugin", "requirements": {"r": ">=4.0", "packages": ["limma", "jsonlite", "QFeatures", "msqrob2"], "rPackagesFile": "r-packages.txt"}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"samples_file": {"stage": 0, "output": "samples"}, "abundance_long_file": {"stage": 0, "output": "abundance_long"}}, "pluginId": "lysoip-reproducibility", "repository": "https://github.com/noatgnu/lysoip-reproducibility-plugin", "requirements": {"python": ">=3.11"}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"differential_expression_file": {"stage": 1, "output": "differential_expression"}}, "pluginId": "lysoip-organelle-specificity", "repository": "https://github.com/noatgnu/lysoip-organelle-specificity-plugin", "requirements": {"python": ">=3.11"}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"gene_lookup_file": {"stage": 1, "output": "differential_expression"}}, "pluginId": "lysoip-go-evidence", "repository": "https://github.com/noatgnu/lysoip-go-evidence-plugin", "requirements": {"python": ">=3.11", "packages": ["goatools>=1.4.0"], "pythonRequirementsFile": "requirements.txt"}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"go_evidence_file": {"stage": 4, "output": "go_evidence"}, "reproducibility_file": {"stage": 2, "output": "reproducibility"}, "organelle_specificity_file": {"stage": 3, "output": "organelle_specificity"}, "differential_expression_file": {"stage": 1, "output": "differential_expression"}}, "pluginId": "lysoip-gating-ranking", "repository": "https://github.com/noatgnu/lysoip-gating-ranking-plugin", "requirements": {"python": ">=3.11", "packages": ["pandas>=2.0.0"]}, "pluginVersion": "1.0.0"}, {"params": {}, "bindings": {"verdict_file": {"stage": 5, "output": "verdict"}}, "pluginId": "lysoip-organelle-coverage", "repository": "https://github.com/noatgnu/lysoip-organelle-coverage-plugin", "requirements": {"python": ">=3.11", "packages": ["scipy>=1.11.0"]}, "pluginVersion": "1.0.0"}], "version": 1, "description": "Full 7-stage lysoip-* pipeline: ingestion -> differential expression -> reproducibility/organelle-specificity/GO-evidence (parallel scorers) -> gating & ranking -> organelle coverage. Stage 0 defaults to the ingestion plugin's bundled example data (generic tidy format); replace with a real experiment before running."}