launch-workflow

# 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 26.04.0 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 list ``` 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 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: ```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 list` 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.