v1.7.0

Fixes from the Barcelona 2026 hackathon's agentic module evaluation (15 runs, 13 PRs, 21 reviews):

• Removed the session-start hook and the using-nf-core-module-dev bootstrap skill. They added context to every session in every project. Routing now lives in the descriptions: nf-module-manager runs for new modules and whole-module updates; small changes are done directly or by the agent that owns the file
• nf-module-manager:
  • new Step 1b: before spawning any agent for a new module, check that the tool has a bioconda, conda-forge or PyPI release; if not, stop and report to the user, since no container can be built without one
  • new Step 3c: for an existing component, nf-test-expert runs the tests of the subworkflows (direct and indirect) and module tests that use it and refreshes their snapshots; nf-module-dev updates a calling subworkflow's main.nf on interface changes
  • new Step 4a: comment review of the diff against AGENTS.md Code Comments, sending long comments back to the owning agent
  • branch guard: one branch (and worktree) per task, with the branch and staged paths checked before every commit. The worktree branches from the freshly fetched nf-core remote (upstream on a fork), and its path is passed to every agent, which now takes the modules repo from its request first
• nf-test-expert:
  • feature-detection rule: every new test must fail without the code it covers. Its snapshot must differ from the existing tests, or a snapshotted boolean must prove the flag reached the tool, and every input branch must be covered
  • sanitizeOutput(process.out) in every test including stubs, process.success inside assertAll (template layout), no separate versions assertion, setup blocks scoped to the test that needs them
  • strict syntax in test code (channel, explicit closure parameters); new Reference: callers check (nf-test test <component>/main.nf --related-tests --follow-dependencies, then --update-snapshot on the legitimately changed ones), run after any change to an existing component, also outside the manager
• nf-module-dev:
  • inputs: one tuple per sample, reference data in its own meta2 tuple, required inputs for databases the tool cannot run without
  • versions: nf-core standard // WARN: Version information not provided by tool on CLI... comment for hardcoded versions; template (R/Python) modules write versions.yml with the interpreter and every loaded package
  • stubs follow the script's input branches, cardinality and validation; output names must not clash with staged inputs; interpolated paths are quoted and zcat -f handles maybe-compressed input
  • reads AGENTS.md Code Comments (as does nf-test-expert)
• nf-secretary: one EDAM term per format the pattern accepts (CSV and bedGraph added to the table), every ext.args option of template modules documented in description, official links and paper DOIs