Update Seqera components to reference workflows from earlier sections

docs/advanced/configuration.md

@@ -14,7 +14,7 @@ This gives us two complications:
 3. Config file specified using the `-c my_config option`
 4. The config file named `nextflow.config` in the current directory
 5. The config file named `nextflow.config` in the workflow project directory
-6. The config file `$HOME/.nextflow/config`
+6. The config file `$HOME/.nextflow/config`, or `$NXF_HOME/.nextflow/config` when `NXF_HOME` is set (see [`NXF` variable docs](reference/env-vars.html#nextflow-settings))
 7. Values defined within the pipeline script itself (e.g. `main.nf`)
 
 !!! note "Precedence is in order of 'distance'"

docs/basic_training/config.md

@@ -15,7 +15,7 @@ When you launch Nextflow, it will look for configuration files in several locati
 3. Config file that are provided using the `-c` option
 4. The config file named `nextflow.config` in the current directory
 5. The config file named `nextflow.config` in the pipeline project directory
-6. The config file `$HOME/.nextflow/config`
+6. The config file `$HOME/.nextflow/config`, or `$NXF_HOME/.nextflow/config` when `NXF_HOME` is set (see [`NXF` variable docs](reference/env-vars.html#nextflow-settings))
 7. Values defined within the pipeline script itself (e.g., `main.nf`)
 
 ## Parameters

docs/hello_nextflow/seqera/01_run_with_cli.md

@@ -41,30 +41,23 @@ Follow these steps to set up your token:
 
 ### 1.2. Run Nextflow CLI with Seqera Platform visualizing and capturing logs
 
-Run a Nextflow workflow with the addition of the `-with-tower` command:
+Run the 'nf-hello-world' workflow you may have encountered in earlier sessions, with the addition of the `-with-tower` command:
 
 ```bash
-nextflow run nextflow-io/hello -with-tower
+nextflow run seqeralabs/nf-hello-world -profile demo --outdir 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
+ N E X T F L O W   ~  version 24.10.2
 
-Launching `https://github.com/nextflow-io/hello` [evil_engelbart] DSL2 - revision: afff16a9b4 [master]
+Launching `https://github.com/seqeralabs/nf-hello-world` [thirsty_hoover] DSL2 - revision: 8274d3d10c [master]
 
-Downloading plugin nf-tower@1.9.1
-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!
+Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/jonathan-manning2/watch/3kLeKzzjHBzB7D
+executor >  local (6)
+[40/c954b7] process > sayHello (2)       [100%] 3 of 3 ✔
+[2f/8162ff] process > convertToUpper (3) [100%] 3 of 3 ✔
 ```
 
 Hold ++ctrl++ or ++cmd++ and click on the link to open it in your browser.
@@ -76,7 +69,11 @@ 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 become tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$HOME/.nextflow/config`.
+Doing that token setup regularly can become tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$NXF_HOME/.nextflow/config`.
+
+!!! hint "Home directory configuration"
+
+    If `NFX_HOME` is not set, these changes would be added to `$HOME/.nextflow/config`
 
 Before we set the configuration, we need to permanently store the token from our environment in Nextflow using a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html):
 
@@ -90,15 +87,15 @@ Make sure your token was saved using:
 nextflow secrets get tower_access_token
 ```
 
-Next, open the Nextflow configuration file located at `$HOME/.nextflow/config`:
+Next, open the Nextflow configuration file located at `$NXF_HOME/.nextflow/config`:
 
 ```bash
-code $HOME/.nextflow/config
+code $NXF_HOME/.nextflow/config
 ```
 
 Then add the following block of configuration:
 
-```groovy title="$HOME/.nextflow/config"
+```groovy title="$NXF_HOME/.nextflow/config"
 tower {
     enabled = true
     endpoint = "https://api.cloud.seqera.io"
@@ -120,20 +117,14 @@ 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!
+  N E X T F L O W   ~  version 24.10.3
 
-Hola world!
+Launching `https://github.com/seqeralabs/nf-hello-world` [golden_moriondo] DSL2 - revision: 8274d3d10c [master]
 
-Hello world!
+Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/jonathan-manning2/watch/1lzYhUz4ziHcYD
+executor >  local (6)
+[30/30a42c] process > sayHello (3)       [100%] 3 of 3 ✔
+[ea/293e98] process > convertToUpper (3) [100%] 3 of 3 ✔
 ```
 
 Note that we are logging to Seqera Platform even though we did not use the `-with-tower` command!
@@ -147,8 +138,8 @@ If you ran your pipeline from the `hello_nextflow` directory, you'll see somethi
 
 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/.nextflow/config` - This is the global configuration file we just added.
+- `/workspace/gitpod/.nextflow/assets/seqeralabs/nf-hello-world/nextflow.config` - This is the `nextflow.config` file from the `seqeralabs/nf-hello-world` 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).

docs/hello_nextflow/seqera/02_run_with_launchpad.md

@@ -10,7 +10,7 @@ Next we want to start using Seqera Platform to launch Nextflow workflows on our
 
 !!! 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.
+    Launch a test run of the seqeralabs/nf-hello-genomics 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
 
@@ -21,18 +21,18 @@ Each user has an allotted 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
+### 2.2. Launch a test run of seqeralabs/nf-hello-genomics 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.
+1. Find the `nf-hello-genomics` pipeline in the list of pipelines (this is the same workflow you may have encountered in the [Hello Genomics](../06_hello_config.md) module).
 2. Click on the `Launch` button to bring up the launch form.
-3. Change the "Workflow run name" to "<username>-rnaseq-test".
+3. Change the "Workflow run name" to "<username>-hellogenomics-test".
 4. Click "Next" to bring up the parameters form.
-5. Find the `trimmer` parameter and change it to `fastp`.
+5. Take a look at the options. Feel free to take a moment to understand them, referring to [Hello Genomics](../06_hello_config.md) as needed.
 6. Click on "Next" to inspect the advanced configuration.
 7. Click "Launch" to start the pipeline!
 
@@ -54,7 +54,7 @@ It may take some time for the pipeline to start running while AWS Batch spins up
 ### 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.
+For example, by searching for `GATK_JOINTGENOTYPING` we can find the main genotyping process that was executed as part of the pipeline.
 
 Click on the task to see the task details: