pegasus-isi/claude-plugin-marketplace

pegasus-review

Review a Pegasus workflow for common pitfalls and best practices

pegasus-scaffold

Create a complete Pegasus workflow project from a pipeline description

pegasus-wrapper

Generate a wrapper script for a single Pegasus pipeline step

pegasus-apptainer

Generate an Apptainer definition file for a Pegasus workflow's tool stack

pegasus-convert

Convert a Snakemake or Nextflow pipeline to a Pegasus workflow

pegasus-debug

Diagnose Pegasus workflow failures from error messages and logs

pegasus-help

Show available Pegasus workflow skills and which one to use

babysit-pr

Autonomously tend one open pegasus PR until merged — address inline review threads, review summaries, and conversation comments (fix → commit → push → re-run e2e → reply), resolve base-branch conflicts, fix red checks, and clean up branch/worktree/labels on…

commit

Create a single commitizen / Conventional Commits git commit that references the issue number. Use ONLY when the user explicitly asks to commit the staged/working changes (e.g. "commit this", /commit). Invocation by an orchestrating skill (ship, work-issue,…

create-issue

Create a GitHub issue from the repo's issue template (bug_report/feature_request), typed/labeled/self-assigned, then an issue-linked branch + git worktree off a chosen base. Use when the user asks to create/open/file a new issue, or invokes /create-issue…

dispatch-issues

Loop A of the autonomous Pegasus dev pipeline — scan claude-labeled issues assigned to you that don't have a PR yet, resume whichever one is in flight, or start the oldest queued one. Designed as a /loop target, runs independently of dispatch-prs (which takes…

dispatch-prs

Loop B of the autonomous Pegasus dev pipeline — babysit every open PR for a claude-labeled issue assigned to you (fix review feedback, resolve conflicts, re-test, clean up on merge), one pass over all of them per wakeup. Designed as a /loop target, runs…

lint

Semantic lint of staged changes for things static analysis misses — spelling/typos, comments that no longer match the code, docstring/signature drift, stale docs & manpages, and house-style idioms (f-strings over .format()/%, logging over print). Use when…

pr

Open a GitHub PR for the current branch, targeting its base — only after e2e passes (or isn't configured at all). Use ONLY when the user explicitly asks to open/create a pull request, or invokes /pr [--base <branch>] [--review-ledger <findings>]. Invocation…

review

Read-only quality gate for the current change — runs simplify, security-review, a general Claude review, Codex review, and Codex adversarial-review against the base branch and consolidates findings. Use when the user asks to review the change/diff before…

run-tests

Trigger and wait for CI on GitLab (scitech-gitlab.isi.edu), or monitor already auto-triggered CI on GitHub Actions — run unit tests, or run e2e/workflow tests. Which one runs depends on the repo — a `.gitlab-ci.yml` at the repo root uses GitLab, a…

ship

Orchestrate the full Pegasus dev pipeline for the current change — unit tests, review, commit, push, e2e, PR — pausing at gates. Use ONLY when the user explicitly asks to ship / run the whole pipeline / take a change through to PR, or invokes /ship [--base…

start

Start work on an existing GitHub issue — create an issue-linked branch (via gh issue develop) and a git worktree, off a chosen base. Use when the user asks to start/begin work on an issue, or invokes /start <issue#> [--base <branch>].

test-pkg

Run a package/directory's unit test suite, auto-detecting the test runner (tox, pytest, npm/yarn/pnpm, make, go test) from what's actually present in it — not hardcoded to any one language or tool. Use when the user asks to run or test a specific…

work-issue

Autonomously advance one claude-labeled GitHub issue to its next checkpoint — clarity gate, branch+worktree, implement, lint, unit tests, review --auto, commit, push, e2e — with no human gates (questions go to issue comments). Use when invoked by the…

kiso

Generate a Kiso experiment.yml configuration file for running Pegasus workflows or shell experiments on cloud/edge/local testbeds. Use this skill whenever the user wants to create or edit a Kiso experiment configuration, provision infrastructure for a Pegasus…