Add more missing functionality

Author: ewels

README.md

@@ -46,7 +46,7 @@ $ seqera info
 
 ### Commands
 
-```
+```text
 pipelines      Manage workspace pipelines
 runs           Manage pipeline runs
 compute-envs   Manage compute environments

SDK.md

@@ -71,7 +71,7 @@ from itertools import islice
 first_10 = list(islice(client.pipelines.list(), 10))
 ```
 
-## Workspaces
+## Workspace Parameter
 
 All operations accept an optional `workspace` parameter. If omitted, uses the default workspace.
 
@@ -172,6 +172,9 @@ result = client.pipelines.launch(
     pull_latest=True,
     resume=False,
     stub_run=False,
+    head_job_container="quay.io/seqeralabs/nf-launcher:j17",  # BETA
+    user_secrets=["MY_SECRET"],
+    workspace_secrets=["SHARED_SECRET"],
 )
 ```
 
@@ -270,6 +273,20 @@ new_workflow_id = client.runs.relaunch(
     work_dir="s3://bucket/new-work",
     compute_env="different-ce",
 )
+
+# Relaunch with additional options
+new_workflow_id = client.runs.relaunch(
+    "abc123",
+    resume=True,
+    pull_latest=True,
+    stub_run=False,
+    head_job_container="quay.io/seqeralabs/nf-launcher:j17",  # BETA
+    main_script="main.nf",
+    entry_name="my_workflow",
+    schema_name="nextflow_schema.json",
+    user_secrets=["MY_SECRET"],
+    workspace_secrets=["SHARED_SECRET"],
+)
 ```
 
 ### Dump run details
@@ -861,8 +878,21 @@ studio = client.studios.create(
     gpu=0,
     description="My data analysis environment",
     auto_start=True,  # Start immediately
+    lifespan=24,  # Hours until auto-stop
+    mount_data=[{"dataLinkId": "v1-user-abc123"}],
 )
 print(f"Created studio: {studio.session_id}")
+
+# Create studio and wait for it to be running
+studio = client.studios.create(
+    name="My Analysis Studio",
+    compute_env_id="ce-123",
+    template_url="cr.seqera.io/public/data-studio-jupyter:1.0",
+    auto_start=True,
+    wait="RUNNING",  # Wait for studio to reach RUNNING status
+    wait_timeout=600,  # Max seconds to wait (default 600)
+)
+print(f"Studio running: {studio.status}")
 ```
 
 ### Create studio from existing
@@ -874,8 +904,20 @@ studio = client.studios.create_from_existing(
     parent_studio_id="parent-studio-id",
     parent_checkpoint_id=123,  # Optional, uses most recent if not specified
     auto_start=True,
+    lifespan=48,  # Hours until auto-stop
+    mount_data=[{"dataLinkId": "v1-user-abc123"}],
 )
 print(f"Cloned studio: {studio.session_id}")
+
+# Clone and wait for running status
+studio = client.studios.create_from_existing(
+    name="Cloned Studio",
+    parent_studio_id="parent-studio-id",
+    auto_start=True,
+    wait="RUNNING",
+    wait_timeout=600,
+)
+print(f"Cloned studio running: {studio.status}")
 ```
 
 ---

USAGE.md

@@ -256,6 +256,21 @@ $ seqera launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_
 
 > **Note**: CLI users are bound to the same user permissions that apply in the Platform UI. Launch users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines.
 
+### Additional launch options
+
+The `launch` command supports additional options for advanced use cases:
+
+```console
+$ seqera launch my_pipeline \
+    --launch-container="quay.io/seqeralabs/nf-launcher:j17" \
+    --user-secrets="MY_SECRET,OTHER_SECRET" \
+    --workspace-secrets="SHARED_SECRET"
+```
+
+- `--launch-container`: Specify a custom container image for the Nextflow head job (BETA feature)
+- `--user-secrets`: Comma-separated list of user secrets to make available during pipeline execution
+- `--workspace-secrets`: Comma-separated list of workspace secrets to make available during pipeline execution
+
 ## Runs
 
 Run `seqera runs -h` to view supported runs operations.
@@ -386,6 +401,37 @@ $ seqera runs list --filter="*man/rnaseq-*"
 
 Run `seqera runs relaunch -h` to view all the required and optional fields for relaunching a run in a workspace.
 
+```console
+$ seqera runs relaunch -i 5z4AMshti4g0GK
+
+  Workflow 6ABCxX0vCX8xhx submitted at user workspace.
+
+    https://cloud.seqera.io/user/abhinav/watch/6ABCxX0vCX8xhx
+```
+
+Additional options for relaunch:
+
+```console
+$ seqera runs relaunch -i 5z4AMshti4g0GK \
+    --no-resume \
+    --pull-latest \
+    --launch-container="quay.io/seqeralabs/nf-launcher:j17" \
+    --main-script="custom_main.nf" \
+    --entry-name="my_workflow" \
+    --user-secrets="MY_SECRET" \
+    --workspace-secrets="SHARED_SECRET"
+```
+
+- `--no-resume`: Start fresh instead of resuming from the previous run
+- `--pull-latest`: Pull the latest pipeline code before running
+- `--stub-run`: Execute in stub/dry-run mode
+- `--launch-container`: Custom container for the Nextflow head job (BETA)
+- `--main-script`: Main script file if different from main.nf
+- `--entry-name`: Main workflow name for DLS2 syntax
+- `--schema-name`: Schema name for the pipeline
+- `--user-secrets`: Comma-separated user secrets for the execution
+- `--workspace-secrets`: Comma-separated workspace secrets for the execution
+
 ### Cancel a run
 
 Run `seqera runs cancel -h` to view all the required and optional fields for canceling a run in a workspace.
@@ -441,6 +487,7 @@ $ seqera runs task -i 5z4AMshti4g0GK -t 1
 ### Download log files
 
 Download workflow or task log files from a run. Available file types:
+
 - **stdout** - Standard output (workflow: `nf-{id}.txt`, task: `.command.out`)
 - **log** - Log file (workflow: `nf-{id}.log`, task: `.command.log`)
 - **stderr** - Standard error (task only: `.command.err`)
@@ -814,11 +861,22 @@ $ seqera studios add -n my-studio -c my-compute-env --template Jupyter \
     --description "My analysis studio" \
     --labels "project=myproject" \
     --auto-start \
+    --lifespan 24 \
+    --mount-data-ids v1-user-abc123 \
+    --wait RUNNING \
     -w 12345
 
   Studio 'abc123' created and started at [myorg / myworkspace] workspace
 ```
 
+Additional studio options:
+
+- `--lifespan`: Hours until the studio automatically stops
+- `--mount-data-ids`: Data link IDs to mount (can be specified multiple times)
+- `--mount-data`: Data link names to mount (can be specified multiple times)
+- `--mount-data-uris`: Data link URIs to mount (can be specified multiple times)
+- `--wait`: Wait for the studio to reach a specific status (e.g., `RUNNING`)
+
 ### Add a studio from existing
 
 Create a new studio from an existing studio's checkpoint (preserving state/data).
@@ -837,6 +895,25 @@ $ seqera studios add-as-new -n cloned-studio --parent-name "My Studio" --parent-
   Studio 'def456' created at [myorg / myworkspace] workspace
 ```
 
+With additional options:
+
+```console
+$ seqera studios add-as-new -n cloned-studio -p parent-studio-id \
+    --lifespan 48 \
+    --mount-data-ids v1-user-abc123 \
+    --auto-start \
+    --wait RUNNING \
+    -w 12345
+
+  Studio 'def456' created and started at [myorg / myworkspace] workspace
+```
+
+- `--lifespan`: Hours until the studio automatically stops
+- `--mount-data-ids`: Data link IDs to mount (can be specified multiple times)
+- `--mount-data`: Data link names to mount (can be specified multiple times)
+- `--mount-data-uris`: Data link URIs to mount (can be specified multiple times)
+- `--wait`: Wait for the studio to reach a specific status (e.g., `RUNNING`)
+
 ### Delete a studio
 
 Run `seqera studios delete -h` to view all the required and optional fields for deleting a studio.

src/seqera/commands/launch.py

@@ -308,6 +308,25 @@ def launch(
         str | None,
         typer.Option("--wait", help="Wait for completion (optional)"),
     ] = None,
+    launch_container: Annotated[
+        str | None,
+        typer.Option(
+            "--launch-container", help="Container to be used to run the Nextflow head job (BETA)"
+        ),
+    ] = None,
+    user_secrets: Annotated[
+        str | None,
+        typer.Option(
+            "--user-secrets", help="User secrets (comma-separated) for the pipeline execution"
+        ),
+    ] = None,
+    workspace_secrets: Annotated[
+        str | None,
+        typer.Option(
+            "--workspace-secrets",
+            help="Workspace secrets (comma-separated) for the pipeline execution",
+        ),
+    ] = None,
 ) -> None:
     """Launch a pipeline."""
     try:
@@ -423,6 +442,19 @@ def launch(
             label_ids = resolve_labels(client, label_names, workspace_id)
             launch_payload["labelIds"] = label_ids
 
+        # Handle launch container (BETA)
+        if launch_container:
+            launch_payload["headJobContainer"] = launch_container
+
+        # Handle secrets
+        if user_secrets:
+            secret_names = [s.strip() for s in user_secrets.split(",")]
+            launch_payload["userSecrets"] = secret_names
+
+        if workspace_secrets:
+            secret_names = [s.strip() for s in workspace_secrets.split(",")]
+            launch_payload["workspaceSecrets"] = secret_names
+
         # Submit launch
         post_params = {}
         if workspace_id:

src/seqera/commands/runs/__init__.py

@@ -363,6 +363,49 @@ def relaunch_run(
         str | None,
         typer.Option("--profile", help="Nextflow profile(s) (comma-separated)"),
     ] = None,
+    launch_container: Annotated[
+        str | None,
+        typer.Option(
+            "--launch-container", help="Container to be used to run the Nextflow head job (BETA)"
+        ),
+    ] = None,
+    pull_latest: Annotated[
+        bool | None,
+        typer.Option("--pull-latest", help="Pull latest repository version before running"),
+    ] = None,
+    stub_run: Annotated[
+        bool | None,
+        typer.Option(
+            "--stub-run", help="Execute workflow replacing process scripts with command stubs"
+        ),
+    ] = None,
+    main_script: Annotated[
+        str | None,
+        typer.Option("--main-script", help="Pipeline main script file if different from main.nf"),
+    ] = None,
+    entry_name: Annotated[
+        str | None,
+        typer.Option(
+            "--entry-name", help="Main workflow name to be executed when using DLS2 syntax"
+        ),
+    ] = None,
+    schema_name: Annotated[
+        str | None,
+        typer.Option("--schema-name", help="Schema name"),
+    ] = None,
+    user_secrets: Annotated[
+        str | None,
+        typer.Option(
+            "--user-secrets", help="User secrets (comma-separated) for the pipeline execution"
+        ),
+    ] = None,
+    workspace_secrets: Annotated[
+        str | None,
+        typer.Option(
+            "--workspace-secrets",
+            help="Workspace secrets (comma-separated) for the pipeline execution",
+        ),
+    ] = None,
 ) -> None:
     """Relaunch a pipeline run."""
     from pathlib import Path
@@ -469,14 +512,33 @@ def relaunch_run(
             "paramsText": params_text,
             "preRunScript": pre_run_script,
             "postRunScript": post_run_script,
-            "mainScript": launch.get("mainScript"),
-            "entryName": launch.get("entryName"),
-            "schemaName": launch.get("schemaName"),
+            "mainScript": main_script if main_script else launch.get("mainScript"),
+            "entryName": entry_name if entry_name else launch.get("entryName"),
+            "schemaName": schema_name if schema_name else launch.get("schemaName"),
             "resume": not no_resume,
-            "pullLatest": launch.get("pullLatest"),
-            "stubRun": launch.get("stubRun"),
+            "pullLatest": pull_latest if pull_latest is not None else launch.get("pullLatest"),
+            "stubRun": stub_run if stub_run is not None else launch.get("stubRun"),
         }
 
+        # Handle launch container (BETA)
+        if launch_container:
+            launch_request["headJobContainer"] = launch_container
+        elif launch.get("headJobContainer"):
+            launch_request["headJobContainer"] = launch.get("headJobContainer")
+
+        # Handle secrets
+        if user_secrets:
+            secret_names = [s.strip() for s in user_secrets.split(",")]
+            launch_request["userSecrets"] = secret_names
+        elif launch.get("userSecrets"):
+            launch_request["userSecrets"] = launch.get("userSecrets")
+
+        if workspace_secrets:
+            secret_names = [s.strip() for s in workspace_secrets.split(",")]
+            launch_request["workspaceSecrets"] = secret_names
+        elif launch.get("workspaceSecrets"):
+            launch_request["workspaceSecrets"] = launch.get("workspaceSecrets")
+
         if name:
             launch_request["runName"] = name