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Remove lab-specific content from the perturbseq-hypotheses skill - #24
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Clears the 15 hits from tools/check_no_lab_specific_content.py on main, all in C_Annotation/agent/perturbseq-hypotheses-skill/. - setup_sterile_run.sh: remote manifest inputs use a `remote:` prefix (was `sherlock:`); fetch_inputs.sh reads the host from STERILE_RUN_REMOTE instead of a hardcoded DTN login, and stops with a clear message when it is unset. - Wording-only: cluster, scratch, dataset and email examples in SKILL.md, failure-modes.md, check_for_leaked_terms.py and verify_citations.py. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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Summary
tools/check_no_lab_specific_content.py(CI guard) failed onmainwith 15 hits, all insrc/Stage3_Interpretation/C_Annotation/agent/perturbseq-hypotheses-skill/(added in966a19a). This clears them. Supersedes #18, whose changes were already onmainor in filesmaindeleted.Changes
setup_sterile_run.sh(only change in behavior): remote manifest inputs use aremote:prefix (wassherlock:).fetch_inputs.shreads the SSH host fromSTERILE_RUN_REMOTEinstead of a hardcoded login, and stops with a clear message when it is unset.SKILL.md,references/failure-modes.md,check_for_leaked_terms.py,verify_citations.py.Testing
tools/check_no_lab_specific_content.py: no hits.bash -n/py_compileon the edited scripts.setup_sterile_run.shin a temp dir with one local and oneremote:input. The local file was copied,fetch_inputs.shheld the rightscpline, and withSTERILE_RUN_REMOTEunset it stopped before any SSH.🤖 Generated with Claude Code