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launch-workflow

Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to S

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Prix non confirmé★ 21 Stars GitHubRegistre mis à jour · 14 sept. 2026agent-skill

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Launch Pipeline on Seqera Platform

Launch Nextflow pipeline executions on cloud (AWS, Google Cloud, Azure) and HPC clusters (Slurm, LSF, etc.) through Seqera Platform. Seqera Platform manages the target compute environment, executes the pipeline from a remote Git repository, and provides monitoring.

Requires Nextflow 26.04 or later (for the nextflow auth and nextflow launch commands).

Main Flow

Configure the compute environment — select a Seqera Platform compute environment for the target cloud or cluster.
Ensure the pipeline is in a remote Git repository — Seqera Platform launches pipelines from GitHub (or a compatible Git host such as GitLab or Bitbucket). If the local pipeline is not yet hosted, assist the user in setting up the repository.
Upload local changes — push any uncommitted local changes to the remote so the launched run reflects the user's current code.
Launch with nextflow launch — submit the pipeline by passing the Git repository URL and the expected parameters.

Step 1: Authenticate with Seqera Platform

Check whether the user is already authenticated:

nextflow auth status

If not authenticated, sign in:

nextflow auth login

This opens a browser for authentication. Wait for the user to complete the login flow before proceeding.

Step 2: Configure the Compute Environment

List available compute environments using the Seqera API:

call_seqera_api(
  service: "platform",
  api_name: "platform_list_compute_envs",
  parameters: {}
)

Selecting the compute environment:

Present the available compute environments to the user (name, platform type, region/cluster).
If multiple environments are available, ask the user which one to use.
If only one is available, propose it and ask for confirmation.
Confirm the selected compute environment with the user before launching.

Step 3: Ensure the Pipeline Is in a Remote Git Repository

Seqera Platform launches pipelines from a remote Git URL — it cannot launch directly from a local path. Verify the pipeline directory is a Git repository connected to a remote on GitHub (or a compatible host like GitLab or Bitbucket).

Check the current state:

git remote -v
git status

If the pipeline is not yet a Git repository or has no remote, assist the user in setting it up:

Initialize the repository if needed:

git init
git add .
git commit -m "Initial pipeline commit"

Help the user create a remote repository (e.g., on GitHub via gh repo create) or ask for an existing remote URL.

Add the remote and push:

git remote add origin <repo-url>
git push -u origin main

Step 4: Upload Local Changes

Before launching, push any local changes so the remote reflects the code that should run:

git status
git add <files>
git commit -m "<message>"
git push

If the working tree is clean and the local branch is in sync with the remote, skip this step.

Step 5: Launch the Pipeline

Use nextflow launch with the Git repository URL and parameters:

nextflow launch <git-repo-url> \
  -r <revision> \
  --input <input> \
  --outdir <outdir> \
  [additional --params...]

Examples

Launch a pipeline from GitHub:

nextflow launch https://github.com/org/pipeline \
  -r main \
  --input samplesheet.csv \
  --outdir s3://bucket/results

Launch an nf-core pipeline:

nextflow launch https://github.com/nf-core/rnaseq \
  -r 3.14.0 \
  --input samplesheet.csv \
  --outdir s3://bucket/results \
  --genome GRCh38

Key options

Option	Description
`-r <revision>`	Pipeline version, branch, or tag
`--input`	Input samplesheet or data
`--outdir`	Output directory (cloud storage when running on cloud CEs)
`-params-file params.yml`	Parameters file
`-resume`	Resume a previous execution

Step 6: Monitor the Execution

nextflow launch returns a run URL on Seqera Platform. Present this URL to the user so they can monitor progress in the Platform UI.

Critical Rules

AUTHENTICATE first — check nextflow auth status before attempting to launch.
CONFIRM the compute environment — always show the user the selected CE before launching.
REQUIRE a remote Git repository — the pipeline must be hosted on GitHub or a compatible Git host. If not, help the user set it up before launching.
PUSH local changes first — the launched run uses the remote code, so local edits must be committed and pushed.
PASS the Git repository URL to nextflow launch, not a local path.
PIN the revision — always use -r to target a specific branch, tag, or commit for reproducibility.
USE cloud storage for --outdir when the target CE runs on a cloud platform (s3://, gs://, az://).
PRESENT the run URL returned by nextflow launch so the user can monitor the run.

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Métadonnées du fichier

name: launch-workflow
description: Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Seqera Platform.
allowed-tools: Bash, Read, Glob, mcp__seqera__search_seqera_api, mcp__seqera__call_seqera_api

Voir le texte original

---
name: launch-workflow
description: Launch Nextflow pipeline executions on cloud and HPC clusters via Seqera Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Seqera Platform.
allowed-tools: Bash, Read, Glob, mcp__seqera__search_seqera_api, mcp__seqera__call_seqera_api
---

# Launch Pipeline on Seqera Platform

**Requires Nextflow 26.04 or later** (for the `nextflow auth` and `nextflow launch` commands).

## Main Flow

1. **Configure the compute environment** — select a Seqera Platform compute environment for the target cloud or cluster.
2. **Ensure the pipeline is in a remote Git repository** — Seqera Platform launches pipelines from GitHub (or a compatible Git host such as GitLab or Bitbucket). If the local pipeline is not yet hosted, assist the user in setting up the repository.
3. **Upload local changes** — push any uncommitted local changes to the remote so the launched run reflects the user's current code.
4. **Launch with `nextflow launch`** — submit the pipeline by passing the Git repository URL and the expected parameters.

## Step 1: Authenticate with Seqera Platform

Check whether the user is already authenticated:

```bash
nextflow auth status
```

If not authenticated, sign in:

```bash
nextflow auth login
```

This opens a browser for authentication. Wait for the user to complete the login flow before proceeding.

## Step 2: Configure the Compute Environment

List available compute environments using the Seqera API:

```
call_seqera_api(
service: "platform",
api_name: "platform_list_compute_envs",
parameters: {}
)
```

Selecting the compute environment:

1. Present the available compute environments to the user (name, platform type, region/cluster).
2. If multiple environments are available, ask the user which one to use.
3. If only one is available, propose it and ask for confirmation.
4. Confirm the selected compute environment with the user before launching.

## Step 3: Ensure the Pipeline Is in a Remote Git Repository

Check the current state:

```bash
git remote -v
git status
```

**If the pipeline is not yet a Git repository or has no remote**, assist the user in setting it up:

1. Initialize the repository if needed:
```bash
git init
git add .
git commit -m "Initial pipeline commit"
```
2. Help the user create a remote repository (e.g., on GitHub via `gh repo create`) or ask for an existing remote URL.
3. Add the remote and push:
```bash
git remote add origin <repo-url>
git push -u origin main
```

## Step 4: Upload Local Changes

Before launching, push any local changes so the remote reflects the code that should run:

```bash
git status
git add <files>
git commit -m "<message>"
git push
```

If the working tree is clean and the local branch is in sync with the remote, skip this step.

## Step 5: Launch the Pipeline

Use `nextflow launch` with the Git repository URL and parameters:

```bash
nextflow launch <git-repo-url> \
-r <revision> \
--input <input> \
--outdir <outdir> \
[additional --params...]
```

### Examples

**Launch a pipeline from GitHub:**
```bash
nextflow launch https://github.com/org/pipeline \
-r main \
--input samplesheet.csv \
--outdir s3://bucket/results
```

**Launch an nf-core pipeline:**
```bash
nextflow launch https://github.com/nf-core/rnaseq \
-r 3.14.0 \
--input samplesheet.csv \
--outdir s3://bucket/results \
--genome GRCh38
```

### Key options

| Option | Description |
|--------|-------------|
| `-r <revision>` | Pipeline version, branch, or tag |
| `--input` | Input samplesheet or data |
| `--outdir` | Output directory (cloud storage when running on cloud CEs) |
| `-params-file params.yml` | Parameters file |
| `-resume` | Resume a previous execution |

## Step 6: Monitor the Execution

`nextflow launch` returns a run URL on Seqera Platform. Present this URL to the user so they can monitor progress in the Platform UI.

## Critical Rules

1. **AUTHENTICATE first** — check `nextflow auth status` before attempting to launch.
2. **CONFIRM the compute environment** — always show the user the selected CE before launching.
3. **REQUIRE a remote Git repository** — the pipeline must be hosted on GitHub or a compatible Git host. If not, help the user set it up before launching.
4. **PUSH local changes first** — the launched run uses the remote code, so local edits must be committed and pushed.
5. **PASS the Git repository URL** to `nextflow launch`, not a local path.
6. **PIN the revision** — always use `-r` to target a specific branch, tag, or commit for reproducibility.
7. **USE cloud storage for `--outdir`** when the target CE runs on a cloud platform (s3://, gs://, az://).
8. **PRESENT the run URL** returned by `nextflow launch` so the user can monitor the run.

Examiner la source

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Licence: Apache-2.0
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Réviser avant installation: Éviter l’installation automatique

Licence: Apache-2.0

Dependency or permission surface needs review
Permission surface may require sandboxing
Financial research output is not financial advice; require human review before any live investment decision
Low GitHub adoption signal
L’approbation de revue IA est absente
Financial research output is not financial advice; require human review before any live investment decision.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
GitHub adoption: 21 GitHub stars
Stars/forks activity: 21 stars, 1 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

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Les outils sont des indications de métadonnées, pas une compatibilité testée. Les prompts sont des suggestions.

Commencer par une petite tâche

1Lisez la source et confirmez entrées, résultats, dépendances et permissions.
2Demandez un plan à l’agent. Approuvez la configuration et les coûts avant un test isolé.
3Vérifiez résultats et fichiers modifiés. Signalez uniquement ce qui a été exécuté et conservez la révision source.

Vérifiez les dépendances, clés API et frais externes dans la source. Un dépôt public ne rend pas tous les services gratuits.

Source et conseils d’utilisation

RépertoriéContrôle statique

Métadonnées et examens sont indicatifs. Popularité, découverte et exécution réussie sont des faits distincts.

Dépôt source: nextflow-io/agent-skills
Licence: Apache-2.0
Version: Unknown
Dernier push GitHub: 5 août 2026
Registre mis à jour: 14 sept. 2026
Chemin des instructions: skills/launch-workflow/SKILL.md @ a19bbe21fc19

Version déclarée dans le registre ; vérifiez les versions de la source.

Qualité

49/100

Revue nécessaire

Confiance

57/100

Do not auto-install

Audit

67/100

Revue nécessaire

Ouvrir l’audit complet Voir le rapport d’évaluation

Dependency or permission surface needs review
Permission surface may require sandboxing
Financial research output is not financial advice; require human review before any live investment decision
Low GitHub adoption signal
L’approbation de revue IA est absente
Financial research output is not financial advice; require human review before any live investment decision.
Quality score needs review
Permission surface needs review: secrets or environment access, shell or command execution
GitHub adoption: 21 GitHub stars
Stars/forks activity: 21 stars, 1 forks; issue activity unavailable in current metadata
Dependency/runtime risk: command execution surface, credential or environment access
Permission surface: secrets or environment access, shell or command execution

Verified installs: —
Résultats: —

Copier ne signifie pas installer. Les compteurs nécessitent un rapport de réussite et ne garantissent pas la qualité globale.

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    "requires_resolve_event_id": true,
    "event_id_source": "Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.",
    "expected_outcomes": [
      "success",
      "failed",
      "not_relevant",
      "blocked_by_risk",
      "setup_required"
    ],
    "payload_template": {
      "event_id": "<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>",
      "skill_slug": "nextflow-io-launch-workflow",
      "task": "Use launch-workflow in an agent workflow",
      "agent": "codex",
      "outcome": "success",
      "install_used": true,
      "risk_blocked": false,
      "setup_required": false,
      "task_success": true,
      "output_quality": 4,
      "error_type": null,
      "human_review_required": false,
      "workspace": "sandbox",
      "time_to_useful_ms": 120000,
      "notes": "Report the smallest successful task, setup friction, files touched, and risk notes."
    }
  },
  "endpoints": {
    "web": "https://www.openagentskill.com/skills/nextflow-io-launch-workflow",
    "api": "https://www.openagentskill.com/api/agent/skills/nextflow-io-launch-workflow",
    "audit": "https://www.openagentskill.com/skills/nextflow-io-launch-workflow/audit",
    "eval": "https://www.openagentskill.com/api/agent/evals?slug=nextflow-io-launch-workflow&task=Use%20launch-workflow%20in%20an%20agent%20workflow&max_risk=medium",
    "resolve": "https://www.openagentskill.com/api/agent/resolve?task=Use%20launch-workflow%20in%20an%20agent%20workflow&agent=codex&max_risk=medium",
    "receipt": "https://www.openagentskill.com/api/agent/receipt?task=Use%20launch-workflow%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text",
    "install": "https://www.openagentskill.com/api/skills/nextflow-io-launch-workflow/install",
    "manifest": "https://www.openagentskill.com/api/registry/manifest/nextflow-io-launch-workflow"
  }
}

Pour le créateur

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Cette fiche a été indexée à partir de sources publiques et n’est pas marquée officielle tant qu’une revendication de mainteneur n’est pas approuvée.

Créateur: nextflow-io
Source: nextflow-io/agent-skills
Indexé par: Index communautaire OpenAgentSkill

L’attribution renvoie au dépôt public ou au profil du créateur. Les créateurs peuvent revendiquer la fiche pour mettre à jour les signaux de propriété.

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