Set up runs, diagnose failures and explore results of the smORF-Bullpen pipeline
Plugin smorf-bullpen from marketplace smorf-bullpen in brendan-miller-salk/smORF-Bullpen. Commands read from the repo's manifest — 19 days ago.
resultsExplain and query the results of a finished smORF-Bullpen run (orfs.csv, summary.csv, counts.tsv, smORF sets, QC reports). Use when the user asks what a run found, how many smORFs passed, why an ORF was excluded, or wants to filter ORFs by type, conservation, UniProt match or expression.
setupSet up and launch a smORF-Bullpen run. Use when the user wants to run smORF-Bullpen on their Ribo-seq FASTQs or annotate an existing ORF GTF, needs a run directory, samplesheet or config, wants help choosing modules, or wants to dry-run or submit the pipeline.
statusCheck on a smORF-Bullpen run and diagnose failures. Use when the user asks whether their run is still going, how far along it is, why it failed or stopped, or how to resume it.
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