🚧 wip(hello_seqera): initial outline of content

kenibrewer · kenibrewer · commit 6c172f3a3d05 · 2024-10-25T10:41:02.000-07:00
diff --git a/docs/hello_nextflow/10_hello_seqera.md b/docs/hello_nextflow/10_hello_seqera.md
@@ -16,9 +16,17 @@ You'll learn how to use Seqera Platform within Nextflow CLI, the Seqera Platform
 
 You can use Seqera Platform via either the **CLI**, through the **online GUI** or through the **API**.
 
-## 1. Use Seqera Platform to capture and monitor Nextflow jobs launched from the CLI
+--8<-- "docs/hello_nextflow/seqera/01_run_with_cli.md"
 
---8<-- "./seqera/01_run_with_cli.md"
+--8<-- "docs/hello_nextflow/seqera/02_run_with_launchpad.md"
+
+--8<-- "docs/hello_nextflow/seqera/03_add_compute_environment.md"
+
+--8<-- "docs/hello_nextflow/seqera/03_add_compute_environment.md"
+
+!!! Warning WORK-IN-PROGRESS
+
+    Everything below this note is content that was copied from the original guide and needs to be moved or rewritten into the above subpages.
 
 ## Online GUI
 
@@ -28,27 +36,6 @@ To run using the GUI, there are three main steps:
 2. Create and configure a new [compute environment](https://docs.seqera.io/platform/24.1/compute-envs/overview).
 3. Start [launching pipelines](https://docs.seqera.io/platform/24.1/launch/launchpad#launchpad).
 
-### Configuring your compute environment
-
-Seqera Platform uses the concept of **Compute Environments** to define the execution platform where a workflow will run.
-
-It supports the launching of workflows into a growing number of **cloud** and **on-premise** infrastructures.
-
-![Compute environments](img/compute_env_platforms.png)
-
-Each compute environment must be pre-configured to enable Seqera Platform to submit tasks. You can read more on how to set up each environment using the links below.
-
-!!! tip "The following guides describe how to configure each of these compute environments."
-
-    * [AWS Batch](https://docs.seqera.io/platform/24.1/compute-envs/aws-batch)
-    * [Azure Batch](https://docs.seqera.io/platform/24.1/compute-envs/azure-batch)
-    * [Google Batch](https://docs.seqera.io/platform/24.1/compute-envs/google-cloud-batch)
-    * [Google Life Sciences](https://docs.seqera.io/platform/24.1/compute-envs/google-cloud-lifesciences)
-    * [HPC (LSF, Slurm, Grid Engine, Altair PBS Pro)](https://docs.seqera.io/platform/24.1/compute-envs/hpc)
-    * [Amazon Kubernetes (EKS)](https://docs.seqera.io/platform/24.1/compute-envs/eks)
-    * [Google Kubernetes (GKE)](https://docs.seqera.io/platform/24.1/compute-envs/gke)
-    * [Hosted Kubernetes](https://docs.seqera.io/platform/24.1/compute-envs/k8s)
-
 ### Selecting a default compute environment
 
 If you have more than one **Compute Environment**, you can select which one will be used by default when launching a pipeline.
diff --git a/docs/hello_nextflow/seqera/01_run_with_cli.md b/docs/hello_nextflow/seqera/01_run_with_cli.md
@@ -1,3 +1,5 @@
+## 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/).
 
@@ -11,15 +13,15 @@ Follow these steps to set up your token:
 
 1.  Create a new token by clicking on the **Settings** drop-down menu:
 
-    ![Create a token](img/usage_create_token.png)
+    ![Create a token](seqera/img/usage_create_token.png)
 
 2.  Name your token:
 
-    ![Name your token](img/usage_name_token.png)
+    ![Name your token](seqera/img/usage_name_token.png)
 
 3.  Save your token safely:
 
-    ![Save token](img/usage_token.png)
+    ![Save token](seqera/img/usage_token.png)
 
     !!! note
 
@@ -66,6 +68,94 @@ Hello world!
 Use ++ctrl+click++ or ++cmd+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](img/run_with_tower.png)
+![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 logging by default
+
+To set up Seqera Platform logging by default, we first want to store our token more securely as a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html).
+
+```bash
+nextflow secrets set tower_access_token "eyxxxxxxxxxxxxxxxQ1ZTE="
+```
+
+You can set up Seqera Platform logging by default by adding the following line to your `nextflow.config` file.
+
+```groovy title="nextflow.config"
+tower {
+    enabled = true
+    endpoint = "https://api.cloud.seqera.io"
+    accessToken = secrets.tower_access_token
+}
+```
+
+Instead of putting this in the `nextflow.config` file of a specific project, you can also put it in the global file located at `$HOME/.nextflow/config`.
+
+```bash
+cat <<EOF >> $HOME/.nextflow/config
+tower {
+    enabled = true
+    endpoint = "https://api.cloud.seqera.io"
+    accessToken = secrets.tower_access_token
+}
+EOF
+```
+
+Run your Nextflow workflows as usual:
+
+```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.
diff --git a/docs/hello_nextflow/seqera/02_run_with_launchpad.md b/docs/hello_nextflow/seqera/02_run_with_launchpad.md
@@ -0,0 +1,5 @@
+## 2 Using Seqera Platform Launchpad to run Nextflow workflows
+
+### 2.1. Navigate to the community/showcase workspace and launch a pipeline
+
+### 2.2. Monitor the execution of a test rna-seq pipeline
diff --git a/docs/hello_nextflow/seqera/03_add_compute_environment.md b/docs/hello_nextflow/seqera/03_add_compute_environment.md
@@ -0,0 +1,26 @@
+## 3. Add a compute environment
+
+In this section, we will simulate setting up a new compute environment to run our pipeline in Seqera Platform Launchpad.
+Seqera Platform uses the concept of **Compute Environments** to define the execution platform where a workflow will run.
+It supports the launching of workflows into a growing number of **cloud** and **on-premise** infrastructures.
+
+![Compute environments](img/compute_env_platforms.png)
+
+Each compute environment must be pre-configured to enable Seqera Platform to submit tasks. You can read more on how to set up each environment using the links below.
+
+!!! tip "The following guides describe how to configure each of these compute environments."
+
+    * [AWS Batch](https://docs.seqera.io/platform/24.1/compute-envs/aws-batch)
+    * [Azure Batch](https://docs.seqera.io/platform/24.1/compute-envs/azure-batch)
+    * [Google Batch](https://docs.seqera.io/platform/24.1/compute-envs/google-cloud-batch)
+    * [Google Life Sciences](https://docs.seqera.io/platform/24.1/compute-envs/google-cloud-lifesciences)
+    * [HPC (LSF, Slurm, Grid Engine, Altair PBS Pro)](https://docs.seqera.io/platform/24.1/compute-envs/hpc)
+    * [Amazon Kubernetes (EKS)](https://docs.seqera.io/platform/24.1/compute-envs/eks)
+    * [Google Kubernetes (GKE)](https://docs.seqera.io/platform/24.1/compute-envs/gke)
+    * [Hosted Kubernetes](https://docs.seqera.io/platform/24.1/compute-envs/k8s)
+
+To practice this process, we will simulate setting up a new slurm compute environment on our gitpod using Tower Agent.
+
+### 3.1. Setup Tower Agent
+
+### 3.2. Add a new Slurm compute environment
diff --git a/docs/hello_nextflow/seqera/04_setup_launchpad.md b/docs/hello_nextflow/seqera/04_setup_launchpad.md
@@ -0,0 +1,11 @@
+## 4. Setup a new pipeline to run in Seqera Platform Launchpad
+
+In this section, we will set up a new pipeline to run in Seqera Platform Launchpad.
+
+### 4.1. Add your Github credentials to your personal workspace in Seqera Platform
+
+### 4.2. Add the pipeline seqeralabs/nf-hello-gatk to your launchpad
+
+### 4.3. Change the branch of the pipeline to nextflow_schema
+
+### 4.4. _Unsuccessfully_ launch a pipeline on our Tower Agent
diff --git a/docs/hello_nextflow/seqera/img/compute_env_platforms.png b/docs/hello_nextflow/seqera/img/compute_env_platforms.png
diff --git a/docs/hello_nextflow/seqera/img/resolved_configuration.png b/docs/hello_nextflow/seqera/img/resolved_configuration.png
