nextflow-io · pditommaso · May 27, 2026
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # Nextflow Claude Code Plugin
 
-Claude Code skills for Nextflow and nf-core bioinformatics workflows, powered by the Seqera MCP server.
+Nextflow and nf-core bioinformatics workflow skills for AI coding agents. Ships as a native Claude Code plugin (auto-updating via the marketplace) and as a single-binary install for Codex, Cursor, Gemini CLI, GitHub Copilot, Goose, Windsurf, and OpenCode via the included [`install.sh`](#other-agents).
 
 ## Skills
 
@@ -13,46 +13,82 @@ Claude Code skills for Nextflow and nf-core bioinformatics workflows, powered by
 
 ## Installation
 
-### 1. Add the marketplace
+### Claude Code
 
-```bash
-/plugin marketplace add nextflow-io/claude-plugin
-```
+The native plugin marketplace gives you automatic updates whenever the upstream skills change.
+
+1. Add the marketplace:
+   ```bash
+   /plugin marketplace add nextflow-io/claude-plugin
+   ```
+2. Install the plugin:
+   ```bash
+   /plugin install nextflow@nextflow-io-claude-plugin
+   ```
+3. Approve the Seqera MCP server when prompted, to enable the skills.
 
-### 2. Install the plugin
+Once installed, invoke the skills with the `nextflow:` namespace:
 
 ```bash
-/plugin install nextflow@nextflow-io-claude-plugin
+/nextflow:install-nextflow
+/nextflow:create-workflow
+/nextflow:run-module
+/nextflow:launch-workflow
 ```
 
-### 3. Approve the Seqera MCP server
-
-When prompted, approve the Seqera MCP server connection to enable the skills.
+### Other agents
 
-## Usage
+The repo ships an `install.sh` script that copies (or symlinks) the SKILL.md files into the target agent's skills directory. The destination follows each agent's own convention — run `./install.sh --list` to see them all.
 
-Once installed, use the skills with the `nextflow:` namespace:
+| Agent | Default destination | Scope |
+|-------|---------------------|-------|
+| `codex` | `~/.codex/skills/` | user-wide |
+| `gemini` | `~/.gemini/skills/` | user-wide |
+| `goose` | `~/.config/goose/skills/` | user-wide |
+| `cursor` | `./.cursor/skills/` | project-scoped (requires Cursor nightly) |
+| `copilot` | `./.github/skills/` | project-scoped |
+| `windsurf` | `./.windsurf/skills/` | project-scoped |
+| `opencode` | `./.opencode/skills/` | project-scoped |
 
 ```bash
-/nextflow:install-nextflow
-/nextflow:create-workflow
-/nextflow:run-module
-/nextflow:launch-workflow
+git clone https://github.com/nextflow-io/claude-plugin
+cd claude-plugin
+
+./install.sh --list                       # show all supported agents and paths
+./install.sh --agent codex                # copy SKILL.md files into the agent's dir
+./install.sh --agent gemini --symlink     # symlink so `git pull` propagates updates
+./install.sh --agent cursor --dry-run     # preview without changing anything
+./install.sh --agent codex --target ~/skills-staging --force
+./install.sh --help
 ```
 
+To update later: `git pull && ./install.sh --agent <name> --force` — or use `--symlink` once and `git pull` is enough.
+
+> The `launch-workflow` skill requires the [Seqera MCP server](https://mcp.seqera.io/mcp). Configure it in your agent before invoking that skill.
+
 ## Local Development
 
-To test the plugin locally without installing:
+To test the plugin locally in Claude Code without installing via the marketplace:
 
 ```bash
 claude --plugin-dir /path/to/claude-plugin
 ```
 
+For other agents, point `install.sh` at a scratch directory and inspect the result:
+
+```bash
+./install.sh --agent codex --target /tmp/nextflow-skills --force
+```
+
 ## Requirements
 
-- [Claude Code](https://claude.ai/code) CLI
+- A coding agent — [Claude Code](https://claude.ai/code), Codex, Cursor, Gemini CLI, or another SKILL.md-compatible harness
 - [Nextflow](https://nextflow.io) **26.04.0 or later** (required for `nextflow module` and `nextflow auth`/`nextflow launch` commands)
 
+## Credits
+
+The cross-agent `install.sh` script's CLI shape was inspired by [alirezarezvani/claude-skills](https://github.com/alirezarezvani/claude-skills/blob/main/scripts/install.sh) (MIT). Credit to its authors.
+
 ## License
 
 Apache-2.0
diff --git a/install.sh b/install.sh
@@ -0,0 +1,233 @@
+#!/usr/bin/env bash
+#
+# install.sh — install the Nextflow agent skills into a SKILL.md-compatible AI coding agent.
+#
+# Claude Code users should use the native plugin marketplace (see README) — it
+# delivers automatic updates. This script targets agents without a native install
+# path: Codex CLI, Cursor, GitHub Copilot, Gemini CLI, Goose, Windsurf, OpenCode.
+#
+# All supported agents expect SKILL.md as-is with YAML frontmatter; no format
+# conversion is performed. The destination layout is always:
+#
+#   <target>/<skill-name>/SKILL.md
+#
+# CLI shape inspired by alirezarezvani/claude-skills (MIT):
+#   https://github.com/alirezarezvani/claude-skills/blob/main/scripts/install.sh
+# Credit to its authors. This is a reduced single-bundle adaptation.
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+SKILLS_SRC="${SCRIPT_DIR}/skills"
+
+AGENT=""
+TARGET=""
+SYMLINK=0
+FORCE=0
+DRY_RUN=0
+
+if [ -t 1 ]; then
+  C_RESET=$'\033[0m'; C_BOLD=$'\033[1m'; C_DIM=$'\033[2m'
+  C_GREEN=$'\033[32m'; C_YELLOW=$'\033[33m'; C_RED=$'\033[31m'
+else
+  C_RESET=''; C_BOLD=''; C_DIM=''
+  C_GREEN=''; C_YELLOW=''; C_RED=''
+fi
+ok()   { printf '%s✓%s %s\n' "$C_GREEN"  "$C_RESET" "$*"; }
+info() { printf '%s•%s %s\n' "$C_DIM"    "$C_RESET" "$*"; }
+warn() { printf '%s!%s %s\n' "$C_YELLOW" "$C_RESET" "$*" >&2; }
+err()  { printf '%s✗%s %s\n' "$C_RED"    "$C_RESET" "$*" >&2; }
+
+# ---- per-agent defaults ----
+# Paths verified against each agent's own documentation:
+#  claude    — Anthropic Claude Code docs (~/.claude/skills/, user-wide)
+#  codex     — OpenAI Codex CLI docs ($CODEX_HOME/skills, default ~/.codex/skills/)
+#  cursor    — cursor.com/changelog/2-4 (.cursor/skills/, currently Cursor nightly)
+#  gemini    — geminicli.com/docs/cli/skills (~/.gemini/skills/ user-wide, .gemini/skills/ project)
+#  copilot   — alirezarezvani/claude-skills INSTALLATION.md (.github/skills/)
+#  goose     — alirezarezvani/claude-skills INSTALLATION.md (~/.config/goose/skills/)
+#  opencode  — alirezarezvani/claude-skills INSTALLATION.md (.opencode/skills/)
+#  windsurf  — alirezarezvani/claude-skills INSTALLATION.md (.windsurf/skills/)
+SUPPORTED_AGENTS="claude codex copilot cursor gemini goose opencode windsurf"
+
+# Resolved absolute path used for the actual install.
+agent_default_path() {
+  case "$1" in
+    claude)   echo "$HOME/.claude/skills" ;;
+    codex)    echo "${CODEX_HOME:-$HOME/.codex}/skills" ;;
+    copilot)  echo "$PWD/.github/skills" ;;
+    cursor)   echo "$PWD/.cursor/skills" ;;
+    gemini)   echo "$HOME/.gemini/skills" ;;
+    goose)    echo "${XDG_CONFIG_HOME:-$HOME/.config}/goose/skills" ;;
+    opencode) echo "$PWD/.opencode/skills" ;;
+    windsurf) echo "$PWD/.windsurf/skills" ;;
+    *) return 1 ;;
+  esac
+}
+
+# Short, conventional form used only for display in --list.
+agent_display_path() {
+  case "$1" in
+    claude)   echo "~/.claude/skills" ;;
+    codex)    echo "~/.codex/skills" ;;
+    copilot)  echo "./.github/skills" ;;
+    cursor)   echo "./.cursor/skills" ;;
+    gemini)   echo "~/.gemini/skills" ;;
+    goose)    echo "~/.config/goose/skills" ;;
+    opencode) echo "./.opencode/skills" ;;
+    windsurf) echo "./.windsurf/skills" ;;
+  esac
+}
+
+agent_scope() {
+  case "$1" in
+    claude|codex|gemini|goose) echo "user-wide" ;;
+    *)                         echo "project-scoped" ;;
+  esac
+}
+
+post_install_hint() {
+  case "$1" in
+    claude)
+      warn "Claude Code's native plugin marketplace is recommended for auto-updates. See README."
+      ;;
+    codex)
+      info "Restart Codex CLI to reload skill metadata."
+      ;;
+    cursor)
+      info "Cursor Agent Skills currently require the nightly channel (Settings → Beta → Nightly)."
+      ;;
+    gemini)
+      info "Gemini CLI also accepts project-scoped skills under .gemini/skills/ — override with --target if needed."
+      ;;
+  esac
+}
+
+list_agents() {
+  printf '%sSupported agents:%s\n' "$C_BOLD" "$C_RESET"
+  printf '  %-10s %-26s %s\n' "AGENT" "DEFAULT PATH" "SCOPE"
+  for a in $SUPPORTED_AGENTS; do
+    printf '  %-10s %-26s %s\n' "$a" "$(agent_display_path "$a")" "$(agent_scope "$a")"
+  done
+  echo
+  echo "All agents use SKILL.md as-is; override the path with --target <dir>."
+}
+
+usage() {
+  cat <<'EOF'
+Usage: install.sh --agent <name> [--target <dir>] [--symlink] [--force] [--dry-run] [-h|--help]
+       install.sh --list
+
+Install Nextflow agent skills (install-nextflow, create-workflow, run-module,
+launch-workflow) into the chosen agent's skills directory.
+
+Options:
+  --agent <name>   Target agent (see --list for the full set)
+  --target <dir>   Override the default destination directory
+  --symlink        Symlink instead of copy, so 'git pull' propagates updates
+  --force          Overwrite existing skills without prompting
+  --dry-run        Print what would happen without changing the filesystem
+  --list           Print all supported agents and their default install paths
+  -h, --help       Show this help
+
+Notes:
+  - All targets use SKILL.md as-is; no format conversion is performed.
+  - For Claude Code, prefer the native plugin marketplace (auto-updates). See README.
+  - Codex CLI requires a restart after install/update to reload skill metadata.
+  - User-wide agents default to ~/.<agent>/skills; project-scoped agents default
+    to ./.<agent>/skills (current working directory).
+
+Examples:
+  ./install.sh --list
+  ./install.sh --agent codex
+  ./install.sh --agent gemini --symlink
+  ./install.sh --agent codex --target ~/skills-staging --force
+  ./install.sh --agent cursor --dry-run
+
+CLI shape inspired by https://github.com/alirezarezvani/claude-skills (MIT).
+EOF
+}
+
+while [ $# -gt 0 ]; do
+  case "$1" in
+    --agent)    AGENT="${2:-}"; shift 2 ;;
+    --target)   TARGET="${2:-}"; shift 2 ;;
+    --symlink)  SYMLINK=1; shift ;;
+    --force)    FORCE=1; shift ;;
+    --dry-run)  DRY_RUN=1; shift ;;
+    --list)     list_agents; exit 0 ;;
+    -h|--help)  usage; exit 0 ;;
+    *) err "Unknown argument: $1"; usage >&2; exit 2 ;;
+  esac
+done
+
+if [ -z "$AGENT" ]; then
+  err "Missing required --agent"
+  usage >&2
+  exit 2
+fi
+
+if [ -z "$TARGET" ]; then
+  if ! TARGET="$(agent_default_path "$AGENT")"; then
+    err "Unknown agent: $AGENT"
+    err "Supported: $SUPPORTED_AGENTS  (run with --list for details)"
+    exit 2
+  fi
+fi
+
+if [ ! -d "$SKILLS_SRC" ]; then
+  err "Source skills/ directory not found: $SKILLS_SRC"
+  exit 1
+fi
+
+if [ "$DRY_RUN" -eq 1 ]; then
+  info "Dry run — no filesystem changes."
+fi
+
+printf '%sInstalling Nextflow skills →%s %s%s%s  %s(%s)%s\n' \
+  "$C_BOLD" "$C_RESET" "$C_DIM" "$TARGET" "$C_RESET" \
+  "$C_DIM" "$(agent_scope "$AGENT")" "$C_RESET"
+
+[ "$DRY_RUN" -eq 0 ] && mkdir -p "$TARGET"
+
+installed=0
+skipped=0
+for skill_dir in "$SKILLS_SRC"/*/; do
+  [ -d "$skill_dir" ] || continue
+  name="$(basename "$skill_dir")"
+  src="${skill_dir%/}"
+  dest="$TARGET/$name"
+
+  if [ -e "$dest" ] || [ -L "$dest" ]; then
+    if [ "$FORCE" -eq 0 ]; then
+      if [ ! -t 0 ]; then
+        warn "$name exists at $dest — not overwriting (non-interactive). Use --force."
+        skipped=$((skipped + 1))
+        continue
+      fi
+      printf '%s%s%s exists at %s. Overwrite? [y/N] ' "$C_BOLD" "$name" "$C_RESET" "$dest"
+      read -r ans
+      case "$ans" in
+        y|Y|yes|YES) ;;
+        *) warn "Skipping $name"; skipped=$((skipped + 1)); continue ;;
+      esac
+    fi
+    [ "$DRY_RUN" -eq 0 ] && rm -rf "$dest"
+  fi
+
+  if [ "$SYMLINK" -eq 1 ]; then
+    [ "$DRY_RUN" -eq 0 ] && ln -s "$src" "$dest"
+    ok "Link $name → $dest"
+  else
+    [ "$DRY_RUN" -eq 0 ] && cp -R "$src" "$dest"
+    ok "Copy $name → $dest"
+  fi
+  installed=$((installed + 1))
+done
+
+suffix=""
+[ "$DRY_RUN" -eq 1 ] && suffix=" — dry run"
+printf '\n%sDone.%s %d installed, %d skipped (agent: %s)%s\n' \
+  "$C_BOLD" "$C_RESET" "$installed" "$skipped" "$AGENT" "$suffix"
+
+post_install_hint "$AGENT"