Hello-seqera

.devcontainer/devcontainer.json

@@ -23,7 +23,7 @@
                 "ms-python.vscode-pylance",
                 "nf-core.nf-core-extensionpack",
                 "nextflow.nextflow",
-                "codezombiech.gitignore",
+                "codezombiech.gitignore"
             ]
         }
     },

.github/gitpod.Dockerfile

@@ -15,14 +15,17 @@ RUN apt-get update --quiet && \
         curl \
         tree \
         graphviz \
-        software-properties-common
-
+        software-properties-common && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # Taken from: https://github.com/nf-core/tools/blob/master/nf_core/gitpod/gitpod.Dockerfile
 # Install Apptainer (Singularity)
 RUN add-apt-repository -y ppa:apptainer/ppa && \
     apt-get update --quiet && \
-    apt install -y apptainer
+    apt install -y apptainer && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
 
 # Install Conda
 RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
@@ -35,6 +38,11 @@ ENV PATH="/opt/conda/bin:$PATH"
 RUN mkdir -p /workspace/data \
     && chown -R gitpod:gitpod /opt/conda /workspace/data
 
+# Install Tower Agent
+RUN curl -fSL https://github.com/seqeralabs/tower-agent/releases/latest/download/tw-agent-linux-x86_64 > tw-agent && \
+    chmod +x tw-agent && \
+    mv tw-agent /usr/local/bin/tw-agent
+
 # Change user to gitpod
 USER gitpod
 

docs/hello_nextflow/10_hello_seqera.md

@@ -1,7 +1,21 @@
+---
+title: "Part 9: Hello Seqera"
+description: Get started with Seqera Platform
+---
+
 # Part 9: Hello Seqera
 
-TODO
+So far we've been running Nextflow workflows on our local machine using the command line interface.
+In this section, we'll introduce you to Seqera Platform, a powerful cloud-based platform for running, monitoring, and sharing Nextflow workflows.
 
----
+!!! tip
+
+    [Sign up](https://cloud.seqera.io/) to try Seqera for free or request a [demo](https://seqera.io/demo/) for deployments in your own on-premise or cloud environment.
+
+You'll learn how to use Seqera Platform within Nextflow CLI, the Seqera Platform GUI, and the API.
+
+You can use Seqera Platform via either the **CLI**, through the **online GUI** or through the **API**.
+
+--8<-- "docs/hello_nextflow/seqera/01_run_with_cli.md"
 
-TODO
+--8<-- "docs/hello_nextflow/seqera/02_run_with_launchpad.md"

docs/hello_nextflow/seqera/01_run_with_cli.md

@@ -0,0 +1,172 @@
+## 1. Use Seqera Platform to capture and monitor Nextflow jobs launched from the CLI
+
+We'll start by using the Nextflow CLI to launch a pipeline and monitor it in Seqera Platform.
+Start by logging into the [Seqera Platform](https://cloud.seqera.io/).
+
+!!! info "Nextflow Tower"
+
+    Seqera Platform was previously known as Nextflow Tower.
+    You'll still see references to the previous name in environment variables and CLI option names.
+
+### 1.1. Set up your Seqera Platform token by exporting it to your environment
+
+Follow these steps to set up your token:
+
+1.  Create a new token by clicking on the **Settings** drop-down menu:
+
+    ![Create a token](seqera/img/usage_create_token.png)
+
+2.  Name your token:
+
+    ![Name your token](seqera/img/usage_name_token.png)
+
+3.  Save your token safely:
+
+    ![Save token](seqera/img/usage_token.png)
+
+    !!! note
+
+        Leave the browser tab with the token open as we will need it once more to store it as a Nextflow secret.
+
+4.  To make your token available to the Nextflow CLI, export it on the command line:
+
+    Open a terminal and type:
+
+    ```bash
+     export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
+    ```
+
+    Where `eyxxxxxxxxxxxxxxxQ1ZTE=` is the token you have just created.
+
+    !!! Warning "Security Note"
+
+        Keep your token secure and do not share it with others.
+        You can add a ++space++ before the `export` command to prevent it from being saved in your shell history.
+
+### 1.2. Run Nextflow CLI with Seqera Platform visualizing and capturing logs
+
+Run a Nextflow workflow with the addition of the `-with-tower` command:
+
+```bash
+nextflow run nextflow-io/hello -with-tower
+```
+
+You will see output similar to the following:
+
+```console title="Output"
+ N E X T F L O W   ~  version 24.04.4
+
+Launching `https://github.com/nextflow-io/hello` [evil_engelbart] DSL2 - revision: afff16a9b4 [master]
+
+Downloading plugin [email protected]
+Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/kenbrewer/watch/5Gs0qqV9Y9rguE
+executor >  local (4)
+[80/810411] process > sayHello (1) [100%] 4 of 4 ✔
+Ciao world!
+
+Bonjour world!
+
+Hola world!
+
+Hello world!
+```
+
+Hold ++ctrl++ or ++cmd++ and click on the link to open it in your browser.
+You'll see the Seqera Platform interface with the job finished and the logs captured.
+
+![Seqera Platform](seqera/img/run_with_tower.png)
+
+You will see and be able to monitor your **Nextflow jobs** in Seqera Platform.
+
+### 1.3. Set up Seqera Platform in Nextflow configuration
+
+Doing that token setup regularly can get a bit tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$HOME/.nextflow/config`.
+
+Before we set the configuration, we need to permanently store the token in Nextflow using a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html):
+
+```bash
+nextflow secrets set tower_access_token "eyxxxxxxxxxxxxxxxQ1ZTE="
+```
+
+Open the Nextflow configuration file located at `$HOME/.nextflow/config`:
+
+```bash
+code $HOME/.nextflow/config
+```
+
+Then add the following block of configuration:
+
+```groovy title="$HOME/.nextflow/config"
+tower {
+    enabled = true
+    endpoint = "https://api.cloud.seqera.io"
+    accessToken = secrets.tower_access_token
+    workspaceId = secrets.tower_workspace_id
+}
+```
+
+!!! hint "Workspace ID and Endpoint"
+
+    We haven't set `secrets.tower_workspace_id` yet, and so Nextflow will fill in an empty string for this value.
+    This will default to the user's workspace in Seqera Platform which is what we want for now.
+
+    The `endpoint` is the URL of the Seqera Platform API.
+    If your institution is running a private instance of Seqera Platform, you will want to change this to the appropriate URL.
+
+Run your Nextflow workflows as before, but without the `-with-tower` command:
+
+```bash
+nextflow run nextflow-io/hello
+```
+
+You will see the following output:
+
+```console title="Output"
+ N E X T F L O W   ~  version 24.04.4
+
+Launching `https://github.com/nextflow-io/hello` [fabulous_euclid] DSL2 - revision: afff16a9b4 [master]
+
+Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/kenbrewer/watch/KYjRktIlOuxrh
+executor >  local (4)
+[71/eaa915] process > sayHello (3) [100%] 4 of 4 ✔
+Ciao world!
+
+Bonjour world!
+
+Hola world!
+
+Hello world!
+```
+
+Note that we are logging to Seqera Platform even though we did not use the `-with-tower` command!
+
+### 1.4. Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline
+
+Click on the link provided in the output to open the Seqera Platform for your run, then click on the `Configuration` tab.
+If you ran your pipeline from the `hello_nextflow` directory, you'll see something like this:
+
+![Seqera Platform Configuration](seqera/img/resolved_configuration.png)
+
+Notice that configuration for our pipeline run is being run pulled from three separate files:
+
+-   `/home/gitpod/.nextflow/config` - This is the global configuration file we just added.
+-   `/home/gitpod/.nextflow/assets/nextflow-io/hello/nextflow.config` - This is the `nextflow.config` file from the `nextflow-io/hello` repository.
+-   `/workspace/gitpod/nf-training/hello-nextflow/nextflow.config` - This is the `nextflow.config` file from our current working directory.
+
+Nextflow resolves these configurations at runtime with a [specific order of precedence](https://www.nextflow.io/docs/latest/config.html#configuration-file).
+The general rule, however, is that more specific configurations override less specific ones, and config/params specified on the CLI will override defaults in the config files.
+
+Helpfully, Seqera Platform shows us the final output of this configuration resolution process which can be very useful for debugging!
+
+### Takeaway
+
+You have learned how to:
+
+-   Set up your Seqera Platform token by exporting it to your environment.
+-   Run Nextflow CLI with Seqera Platform visualizing and capturing logs.
+-   Set up Seqera Platform logging by default.
+-   Use Seqera Platform to explore the resolved configuration of a Nextflow pipeline.
+
+### What's next?
+
+Learn how to launch Nextflow pipelines from Seqera Platform using the Launchpad feature.

docs/hello_nextflow/seqera/02_run_with_launchpad.md

@@ -0,0 +1,85 @@
+## 2 Using Seqera Platform Launchpad to run Nextflow workflows
+
+So far we've been running Nextflow workflows on our local machine using the command line interface but sending the logs to Seqera Platform for monitoring and visualization.
+Next we want to start using Seqera Platform to launch Nextflow workflows on our behalf.
+
+!!! Note "Community Showcase"
+
+    Having a compute environment capable of running Nextflow workflows configured in Seqera Platform is normally a prerequisite for this task.
+    But we want to see how it works before we put in that effort, so we'll start by launching a job in community/showcase workspace which has a compute environment already set up.
+
+!!! tip "Trainer Tip"
+
+    Launch a test run of the nf-core/rnaseq pipeline in the community/showcase workspace prior to starting this session, so you'll have a recent run for participants to inspect.
+
+### 2.1. Navigate to the community/showcase workspace
+
+Seqera Platform has a concept of [**organizations**](https://docs.seqera.io/platform/latest/orgs-and-teams/organizations) and [**workspaces**](https://docs.seqera.io/platform/latest/orgs-and-teams/workspace-management) which are used to organize and share [pipelines](https://docs.seqera.io/platform/latest/launch/launchpad), [compute environments](https://docs.seqera.io/platform/latest/compute-envs/overview), [data](https://docs.seqera.io/platform/latest/data/data-explorer), [credentials](https://docs.seqera.io/platform/latest/credentials/overview), and more.
+The `community/showcase` workspace is a public workspace where you can see some example pipelines and compute environments.
+Each user has an alloted amount of free compute to use in this workspace.
+
+Click on your username in the top left corner of the screen to bring up the list of organizations and workspaces you have access to.
+Select the `community/showcase` workspace.
+
+### 2.2. Launch a test run of nf-core/rnaseq pipeline
+
+In the `community/showcase` workspace, you will see a list of pipelines that have been set up by the workspace owner for you to run.
+Follow these steps to launch a test run of a pipeline:
+
+![Launchpad](seqera/img/launchpad.gif)
+
+1. Find the `nf-core-rnaseq` pipeline in the list of pipelines.
+2. Click on the `Launch` button to bring up the launch form.
+3. Change the "Workflow run name" to "<username>-rnaseq-test".
+4. Click "Next" to bring up the parameters form.
+5. Find the `trimmer` parameter and change it to `fastp`.
+6. Click on "Next" to inspect the advanced configuration.
+7. Click "Launch" to start the pipeline!
+
+!!! Tip
+
+    In the advanced configuration, you'll see a section named "Pre-run script" with a script similar to the following:
+
+    ```bash
+    export NXF_FILE_ROOT=s3://nf-tower-bucket/scratch/$TOWER_WORKFLOW_ID
+    ```
+
+    This is what ensures that everyone's pipeline will write to a unique location in cloud storage despite all having the `outdir` parameter set to `./results`.
+
+### 2.3. Monitor the pipeline run
+
+After launching the pipeline, you will be taken to the pipeline run page where you can monitor the progress of the pipeline.
+It may take some time for the pipeline to start running while AWS Batch spins up the needed resources, so go to the "Runs" tab above the pipeline and open a recent completed (or failed) run by one of your "teammates" in the community.
+
+### 2.4. Inspect a pipeline run
+
+Scroll down to find the list of tasks that were executed in the pipeline run.
+For example, by searching for `fastq` we can find the task `NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP (WT_REP2)` that was executed as part of the pipeline.
+
+Click on the task to see the task details:
+
+![Task details](seqera/img/task_details.png)
+
+1. Find the following details on the "About" page for the the task you're inspecting:
+
+    - [ ] How long did the task script run (not including scheduling time)?
+    - [ ] How many CPUs were allocated to the task?
+    - [ ] What was the virtual machine type that the task ran on?
+    - [ ] What was the estimated cost of the task?
+
+2. Explore the Execution Log tab. What information is available here?
+
+3. Explore the Data Explorer tab. Note that the work directory structure we've seen during local runs is replicated here in cloud storage!
+
+### Takeaway
+
+You have learned how to:
+
+-   Switch between organizations and workspaces in Seqera Platform.
+-   Launch a Nextflow pipeline that ran in the cloud using Seqera Platform.
+-   Monitor the progress of the pipeline run.
+-   Inspect the details of a task that was executed as part of the pipeline.
+
+### Next steps
+
+In the next section, we will learn how to set up a compute environment in Seqera Platform to run our own Nextflow workflows.

mkdocs.yml

@@ -155,6 +155,9 @@ markdown_extensions:
           preserve_tabs: true
     - pymdownx.tabbed:
           alternate_style: true
+    - pymdownx.tasklist:
+          custom_checkbox: true
+          clickable_checkbox: true
     - tables
     - toc:
           title: On this page