New course: Nextflow Triathlon: plain Nextflow + nf-core + Seqera platform

archive/nextflow-run/1-hello.nf

@@ -0,0 +1,42 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    input:
+    val greeting
+
+    output:
+    path 'output.txt'
+
+    script:
+    """
+    echo '${greeting}' > output.txt
+    """
+}
+
+/*
+ * Pipeline parameters
+ */
+params {
+    input: String
+}
+
+workflow {
+
+    main:
+    // emit a greeting
+    sayHello(params.input)
+
+    publish:
+    first_output = sayHello.out
+}
+
+output {
+    first_output {
+        path '1-hello'
+        mode 'copy'
+    }
+}

archive/nextflow-run/data/greetings.csv

@@ -0,0 +1,3 @@
+Hello,English,123
+Bonjour,French,456
+Hola,Spanish,789

archive/nextflow-run/modules/cowpy.nf

@@ -0,0 +1,17 @@
+// Generate ASCII art with cowpy (https://github.com/jeffbuttars/cowpy)
+process cowpy {
+
+    container 'community.wave.seqera.io/library/cowpy:1.1.5--3db457ae1977a273'
+
+    input:
+    path input_file
+    val character
+
+    output:
+    path "cowpy-${input_file}"
+
+    script:
+    """
+    cat ${input_file} | cowpy -c "${character}" > cowpy-${input_file}
+    """
+}

archive/nextflow-run/nextflow.config

@@ -0,0 +1 @@
+docker.enabled = true

archive/nextflow-run/solutions/modules/collectGreetings.nf

@@ -0,0 +1,20 @@
+/*
+ * Collect uppercase greetings into a single output file
+ */
+process collectGreetings {
+
+    input:
+    path input_files
+    val batch_name
+
+    output:
+    path "COLLECTED-${batch_name}-output.txt", emit: outfile
+    path "${batch_name}-report.txt", emit: report
+
+    script:
+    count_greetings = input_files.size()
+    """
+    cat ${input_files} > 'COLLECTED-${batch_name}-output.txt'
+    echo 'There were ${count_greetings} greetings in this batch.' > '${batch_name}-report.txt'
+    """
+}

archive/nextflow-run/solutions/modules/convertToUpper.nf

@@ -0,0 +1,16 @@
+/*
+ * Use a text replacement tool to convert the greeting to uppercase
+ */
+process convertToUpper {
+
+    input:
+    path input_file
+
+    output:
+    path "UPPER-${input_file}"
+
+    script:
+    """
+    cat '${input_file}' | tr '[a-z]' '[A-Z]' > 'UPPER-${input_file}'
+    """
+}

archive/nextflow-run/solutions/modules/sayHello.nf

@@ -0,0 +1,16 @@
+/*
+ * Use echo to print 'Hello World!' to a file
+ */
+process sayHello {
+
+    input:
+    val greeting
+
+    output:
+    path "${greeting}-output.txt"
+
+    script:
+    """
+    echo '${greeting}' > '${greeting}-output.txt'
+    """
+}

docs/en/docs/archive/nextflow_run/00_orientation.md

@@ -0,0 +1,120 @@
+# Getting started
+
+## Start a training environment
+
+To use the pre-built environment we provide on GitHub Codespaces, click the "Open in GitHub Codespaces" button below. For other options, see [Environment options](../../envsetup/index.md).
+
+We recommend opening the training environment in a new browser tab or window (use right-click, ctrl-click or cmd-click depending on your equipment) so that you can read on while the environment loads.
+You will need to keep these instructions open in parallel to work through the course.
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/nextflow-io/training?quickstart=1&ref=master)
+
+### Environment basics
+
+This training environment contains all the software, code and data necessary to work through the training course, so you don't need to install anything yourself.
+
+The codespace is set up with a VSCode interface, which includes a filesystem explorer, a code editor and a terminal shell.
+All instructions given during the course (e.g. 'open the file', 'edit the code' or 'run this command') refer to those three parts of the VScode interface unless otherwise specified.
+
+If you are working through this course by yourself, please acquaint yourself with the [environment basics](../../envsetup/01_setup.md) for further details.
+
+### Version requirements
+
+This training works with Nextflow 25.10.2 or later **with the v2 syntax parser ENABLED**.
+If you are using a local or custom environment, please make sure you are using the correct settings as documented [here](../../info/nxf_versions.md).
+
+## Get ready to work
+
+Once your codespace is running, there are two things you need to do before diving into the training: set your working directory for this specific course, and take a look at the materials provided.
+
+### Set the working directory
+
+By default, the codespace opens with the work directory set at the root of all training courses, but for this retired version of the course, we'll be working in the `archive/nextflow-run/` directory.
+
+Change directory now by running this command in the terminal:
+
+```bash
+cd archive/nextflow-run/
+```
+
+You can set VSCode to focus on this directory, so that only the relevant files show in the file explorer sidebar:
+
+```bash
+code .
+```
+
+!!! tip
+
+    If for whatever reason you move out of this directory (e.g. your codespace goes to sleep), you can always use the full path to return to it, assuming you're running this within the Github Codespaces training environment:
+
+    ```bash
+    cd /workspaces/training/archive/nextflow-run
+    ```
+
+Now let's have a look at the contents.
+
+### Explore the materials provided
+
+You can explore the contents of this directory by using the file explorer on the left-hand side of the training workspace.
+Alternatively, you can use the `tree` command.
+
+Throughout the course, we use the output of `tree` to represent directory structure and contents in a readable form, sometimes with minor modifications for clarity.
+
+Here we generate a table of contents to the second level down:
+
+```bash
+tree . -L 2
+```
+
+??? abstract "Directory contents"
+
+    ```console
+    .
+    ├── 1-hello.nf
+    ├── 2a-inputs.nf
+    ├── 2b-multistep.nf
+    ├── 2c-modules.nf
+    ├── 2d-container.nf
+    ├── 3-main.nf
+    ├── data
+    │   └── greetings.csv
+    ├── modules
+    │   ├── collectGreetings.nf
+    │   ├── convertToUpper.nf
+    │   ├── cowpy.nf
+    │   └── sayHello.nf
+    ├── nextflow.config
+    ├── solutions
+    │   ├── 3-main.nf
+    │   ├── modules
+    │   └── nextflow.config
+    ├── test-params.json
+    └── test-params.yaml
+    ```
+
+Click on the colored box to expand the section and view its contents.
+We use collapsible sections like this to display expected command output as well as directory and file contents in a concise way.
+
+- **The `.nf` files** are workflow scripts that are numbered based on what part of the course they're used in.
+
+- **The file `nextflow.config`** is a configuration file that sets minimal environment properties.
+  You can ignore it for now.
+
+- **The file `greetings.csv`** under `data/` contains input data we'll use in most of the course. It is described in Part 2 (Run pipelines), when we introduce it for the first time.
+
+- **The `test-params.*`** files are configuration files we'll use in Part 3 (Configuration). You can ignore them for now.
+
+- **The `solutions` directory** contains the final state of the workflow and its accessory files (config and modules) that result from completing the course.
+  They are intended to be used as a reference to check your work and troubleshoot any issues.
+
+## Readiness checklist
+
+Think you're ready to dive in?
+
+- [ ] I understand the goal of this course and its prerequisites
+- [ ] My environment is up and running
+- [ ] I've set my working directory appropriately
+
+If you can check all the boxes, you're good to go.
+
+**To continue to [Part 1: Run Basic operations](./01_basics.md), click on the arrow in the bottom right corner of this page.**

docs/en/docs/nextflow_run/01_basics.md → docs/en/docs/archive/nextflow_run/01_basics.md

@@ -111,7 +111,7 @@ If your console output looks something like that, then congratulations, you just
 
     Then you're probably using the older v1 Nextflow language parser.
     This was mentioned at the start of the course, but maybe you missed it.
-    Check the [Nextflow versions](../info/nxf_versions.md) help material.
+    Check the [Nextflow versions](../../info/nxf_versions.md) help material.
 
     In short, if you're using Nextflow `25.10` then you need to enable the v2 language parser:
 
@@ -468,7 +468,7 @@ process sayHello {
 Here we have a **process** called `sayHello` that takes an **input** variable called `greeting` and writes its **output** to a file named `output.txt`.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/sayhello_with_input.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/sayhello_with_input.svg"
 </figure>
 
 This is a very minimal process definition that just contains an `input` definition, an `output` definition and the `script` to execute.

docs/en/docs/nextflow_run/02_pipeline.md → docs/en/docs/archive/nextflow_run/02_pipeline.md

@@ -24,7 +24,7 @@ Hola,Spanish,789
 We've also written an improved version of the original workflow, now called `2a-inputs.nf`, that will read in the CSV file, extract the greetings and write each of them to a separate file.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/hello-pipeline-multi-inputs.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/hello-pipeline-multi-inputs.svg"
 </figure>
 
 Let's run the workflow first, and we'll take a look at the relevant Nextflow code afterward.
@@ -274,7 +274,7 @@ The result is a channel containing `Hello`, `Bonjour`, and `Hola`.
 
     And then we've taken the first element from each of the three rows and loaded them into a Nextflow channel that now contains: `Hello`, `Bonjour`, and `Hola`.
 
-    If you want to understand channels and operators in depth, including how to write them yourself, see [Hello Nextflow Part 2: Hello Channels](../hello_nextflow/02_hello_channels.md#4-read-input-values-from-a-csv-file).
+    If you want to understand channels and operators in depth, including how to write them yourself, see [Hello Nextflow Part 2: Hello Channels](../../hello_nextflow/02_hello_channels.md#4-read-input-values-from-a-csv-file).
 
 #### 1.4.2. Call the process on each greeting
 
@@ -344,7 +344,7 @@ To that end, we provide you with an example workflow that chains together three
 Specifically, we made an expanded version of the workflow called `2b-multistep.nf` that takes each input greeting, converts it to uppercase, then collects all the uppercased greetings into a single output file.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/hello-pipeline-multi-steps.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/hello-pipeline-multi-steps.svg"
 </figure>
 
 As previously, we'll run the workflow first then look at the code to see what is new.
@@ -541,15 +541,15 @@ Let's take a closer look and see if we can identify the most interesting pieces.
 If you're using VSCode with the Nextflow extension, you can get a helpful diagram of how the processes are connected by clicking on the small `DAG preview` link displayed just above the workflow block in any Nextflow script.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/DAG-multistep.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/DAG-multistep.svg"
 </figure>
 
 This gives you a nice overview of how the processes are connected and what they produce.
 
 You see that in addition to the original `sayHello` process, we now also have `convertToUpper` and `collectGreetings`, which match the names of the processes we saw in the console output.
 The two new process definitions are structured in the same way as the `sayHello` process, except `collectGreetings` takes an additional input parameter called `batch` and produces two outputs.
 
-We won't go into the code for each in detail, but if you're curious, you can look up the details in [Part 2 of Hello Nextflow](../hello_nextflow/03_hello_workflow.md).
+We won't go into the code for each in detail, but if you're curious, you can look up the details in [Part 2 of Hello Nextflow](../../hello_nextflow/03_hello_workflow.md).
 
 For now, let's dig into how the processes are connected to one another.
 
@@ -620,13 +620,13 @@ In the context of this workflow, it's taking the three uppercased greetings in t
 That's how we get all the greetings back into the same file.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/with-collect-operator.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/with-collect-operator.svg"
 </figure>
 
 In contrast, if we didn't apply `collect()` to the output of `convertToUpper()` before feeding it to `collectGreetings()`, Nextflow would simply run `collectGreetings()` independently on each greeting, which would not achieve our goal.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/without-collect-operator.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/without-collect-operator.svg"
 </figure>
 
 There are many other [operators](https://nextflow.io/docs/latest/reference/operator.html) available to apply transformations to the contents of channels between process calls.
@@ -756,7 +756,7 @@ There are more sophisticated ways to organize published outputs; we'll touch on
 
 !!! tip "Want to learn more about building workflows?"
 
-    For detailed coverage of building multi-step workflows, see [Hello Nextflow Part 3: Hello Workflow](../hello_nextflow/03_hello_workflow.md).
+    For detailed coverage of building multi-step workflows, see [Hello Nextflow Part 3: Hello Workflow](../../hello_nextflow/03_hello_workflow.md).
 
 ### Takeaway
 
@@ -788,7 +788,7 @@ Now we're going to see what it looks like when the processes are stored in indiv
 We have of course once again prepared a suitable workflow for demonstration purposes, called `2c-modules.nf`, along with a set of modules located in the `modules/` directory.
 
 <figure class="excalidraw">
---8<-- "docs/en/docs/nextflow_run/img/modules.svg"
+--8<-- "docs/en/docs/archive/nextflow_run/img/modules.svg"
 </figure>
 
 ??? abstract "Directory contents"
@@ -1066,7 +1066,7 @@ You see that the filesystem inside the container is different from the filesyste
 
     This effectively establishes a tunnel through the container wall that you can use to access that part of your filesystem.
 
-    This is covered in more detail in [Part 5 of Hello Nextflow](../hello_nextflow/05_hello_containers.md).
+    This is covered in more detail in [Part 5 of Hello Nextflow](../../hello_nextflow/05_hello_containers.md).
 
 #### 4.1.3. Run the `cowpy` tool
 

docs/en/docs/nextflow_run/03_config.md → docs/en/docs/archive/nextflow_run/03_config.md

@@ -11,7 +11,7 @@ By learning to utilize these configuration options effectively, you can take ful
 
 To exercise these elements of configuration, we're going to be running a fresh copy of the workflow we last ran at the end of Part 2 of this training course, renamed `3-main.nf`.
 
-If you're not familiar with the Hello pipeline or you could use a reminder, see [this info page](../info/hello_pipeline.md).
+If you're not familiar with the Hello pipeline or you could use a reminder, see [this info page](../../info/hello_pipeline.md).
 
 ---
 
@@ -1347,7 +1347,7 @@ This means that as long as we distribute any test data files with the workflow c
     We can point to URLs for larger files that are stored externally.
     Nextflow will download them automatically as long as there is an open connection.
 
-    For more details, see the Side Quest [Working with Files](../side_quests/working_with_files/index.md)
+    For more details, see the Side Quest [Working with Files](../../side_quests/working_with_files/index.md)
 
 ### 6.3. Use `nextflow config` to see the resolved configuration
 
@@ -1546,8 +1546,8 @@ You know everything you need to know to get started running and managing Nextflo
 
 That concludes this course, but if you're eager to keep learning, we have two main recommendations:
 
-- If you want to dig deeper into developing your own pipelines, have a look at [Hello Nextflow](../hello_nextflow/index.md), a course for beginners that covers the same general progression as this one but goes into much more detail about channels and operators.
-- If you would like to continue learning how to run Nextflow pipelines without going deeper into the code, have a look at the first part of [Hello nf-core](../hello_nf-core/index.md), which introduces the tooling for finding and running pipelines from the hugely popular [nf-core](https://nf-co.re/) project.
+- If you want to dig deeper into developing your own pipelines, have a look at [Hello Nextflow](../../hello_nextflow/index.md), a course for beginners that covers the same general progression as this one but goes into much more detail about channels and operators.
+- If you would like to continue learning how to run Nextflow pipelines without going deeper into the code, have a look at the first part of [Hello nf-core](../../hello_nf-core/index.md), which introduces the tooling for finding and running pipelines from the hugely popular [nf-core](https://nf-co.re/) project.
 
 Have fun!