Merge pull request #294 from ewels/intro-example-python

Extend the 'Your first script' section.

.github/gitpod.Dockerfile

@@ -3,6 +3,7 @@ FROM gitpod/workspace-base
 USER root
 
 # Install util tools.
+# software-properties-common is needed to add ppa support for Apptainer installation
 RUN apt-get update --quiet && \
     apt-get install --quiet --yes \
         apt-transport-https \
@@ -13,7 +14,8 @@ RUN apt-get update --quiet && \
         wget \
         curl \
         tree \
-        graphviz
+        graphviz \
+        software-properties-common
 
 # Install Conda
 RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
@@ -24,12 +26,11 @@ ENV PATH="/opt/conda/bin:$PATH"
 
 # User permissions
 RUN mkdir -p /workspace/data \
-    && chown -R gitpod:gitpod /workspace/data \
-    && chown -R gitpod:gitpod /opt/conda
+    && chown -R gitpod:gitpod /opt/conda /workspace/data
 
+# Change user to gitpod
 USER gitpod
 
-
 # Uncomment if we need to pin the Nextflow version
 # ENV NXF_EDGE=1
 # ENV NXF_VER=22.09.7-edge
@@ -39,12 +40,20 @@ RUN conda config --add channels defaults && \
     conda config --add channels bioconda && \
     conda config --add channels conda-forge && \
     conda config --set channel_priority strict && \
-    conda install --quiet --yes --name base mamba && \
-    mamba install --quiet --yes --name base \
+    conda update --quiet --yes --all && \
+    conda install --quiet --yes --name base \
+        mamba \
         nextflow \
         nf-core \
+        nf-test \
+        black \
+        prettier \
+        pre-commit \
         pytest-workflow && \
-    mamba clean --all -f -y
+    conda clean --all --force-pkgs-dirs --yes
+
+# Update Nextflow
+RUN nextflow self-update && nextflow -version
 
 RUN unset JAVA_TOOL_OPTIONS
 

.github/workflows/docker.yml

@@ -2,7 +2,7 @@
 # - Only pushes if push or release
 # - Builds without push for PRs to check the Dockerfile
 
-name: Build Docker image
+name: Build GitPod Docker image
 
 on:
     pull_request:
@@ -14,29 +14,29 @@ on:
 jobs:
     push_to_registry:
         if: github.repository == 'nextflow-io/training'
-        name: Build + Push Docker image
+        name: Build + Push Gitpod Docker image
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repo
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Login to GitHub Container Registry
-              uses: docker/login-action@v2
+              uses: docker/login-action@v3
               with:
                   registry: ghcr.io
                   username: ${{ github.repository_owner }}
                   password: ${{ secrets.GITHUB_TOKEN }}
 
             - name: Build / push latest image
-              uses: docker/build-push-action@v3
+              uses: docker/build-push-action@v5
               if: github.event_name != 'release'
               with:
                   file: .github/gitpod.Dockerfile
                   push: ${{ github.event_name == 'push' }}
                   tags: ghcr.io/nextflow-io/training:latest
 
             - name: Push release image
-              uses: docker/build-push-action@v3
+              uses: docker/build-push-action@v5
               if: github.event_name == 'release'
               with:
                   file: .github/gitpod.Dockerfile

.github/workflows/mkdocs-docker.yml

@@ -14,17 +14,17 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Check out the repo
-              uses: actions/checkout@v3
+              uses: actions/checkout@v4
 
             - name: Login to GitHub Container Registry
-              uses: docker/login-action@v2
+              uses: docker/login-action@v3
               with:
                   registry: ghcr.io
                   username: ${{ github.repository_owner }}
                   password: ${{ secrets.GITHUB_TOKEN }}
 
             - name: Build / push latest image
-              uses: docker/build-push-action@v3
+              uses: docker/build-push-action@v5
               with:
                   file: .github/mkdocs.Dockerfile
                   push: ${{ github.event_name == 'push' }}

docs/advanced/setup.md

@@ -158,11 +158,11 @@ The latest releases can be viewed on GitHub [here](https://github.com/nextflow-i
 If you want to use a specific version of Nextflow, you can set the `NXF_VER` variable as shown below:
 
 ```bash
-export NXF_VER=23.04.1
+export NXF_VER=23.10.0
 ```
 
 !!! Note
 
-    This tutorial workshop requires `NXF_VER=23.04.1`, or later. This version will use DSL2 as default.
+    This tutorial workshop requires `NXF_VER=23.10.0`, or later.
 
 Run `nextflow -version` again to confirm that the change has taken effect.

docs/basic_training/intro.md

@@ -142,7 +142,25 @@ workflow { // (18)!
 21. The final output (in the `results_ch` channel) is printed to screen using the `view` operator (appended onto the channel name).
 22. End of the workflow scope.
 
-The use of the operator `.flatten()` here is to split the two files into two separate items to be put through the next process (else they would be treated as a single element).
+This pipeline takes `params.greeting`, which defaults to the string `Hello world!`, and splits it into indiviudual words in the `SPLITLETTERS` process. Each word is written to a separate file, named `chunk_aa`, `chunk_ab`, `chunk_ac`and so on. These files are picked up as the process `output`.
+
+The second process `CONVERTTOUPPER` takes the output channel from the first process as its input.
+The use of the operator `.flatten()` here is to split the two files into two separate items to be put through the this process, else they would be treated as a single element.
+The `CONVERTTOUPPER` process thus launches two tasks, one for each element. The bash script uses `cat` to print the file contents and `tr` to convert to upper-case. It takes the resulting standard-out as the process output channel.
+
+#### Python instead of bash
+
+If you're not completely comfortable with the bash code used in the example, don't worry! You can use whatever programming language you like within Nextflow `script` blocks. For example, here is the same example using Python code:
+
+```python title="nf-training/hello_py.nf" linenums="14"
+--8<-- "nf-training/hello_py.nf:14:18"
+```
+
+```python title="nf-training/hello_py.nf" linenums="30"
+--8<-- "nf-training/hello_py.nf:30:32"
+```
+
+Note that the `$x` and `$y` variables are interpolated by Nextflow, so the resulting Python scripts will have fixed strings here (`#!python x="Hello world!"`).
 
 ### In practice
 

docs/basic_training/setup.fr.md

@@ -162,11 +162,11 @@ Les dernières versions peuvent être consultées sur GitHub [ici](https://githu
 Si vous souhaitez utiliser une version spécifique de Nextflow, vous pouvez définir la variable `NXF_VER` comme indiqué ci-dessous :
 
 ```bash
-export NXF_VER=23.04.1
+export NXF_VER=23.10.0
 ```
 
 !!! Remarque
 
-    Cet atelier tutoriel nécessite `NXF_VER=23.04.1`, ou une version plus récente. Cette version utilise DSL2 par défaut.
+    Cet atelier tutoriel nécessite `NXF_VER=23.10.0`, ou une version plus récente.
 
 Exécutez `nextflow -version` à nouveau pour confirmer que le changement a pris effet.

docs/basic_training/setup.md

@@ -162,11 +162,11 @@ The latest releases can be viewed on GitHub [here](https://github.com/nextflow-i
 If you want to use a specific version of Nextflow, you can set the `NXF_VER` variable as shown below:
 
 ```bash
-export NXF_VER=23.04.1
+export NXF_VER=23.10.0
 ```
 
 !!! Note
 
-    This tutorial workshop requires `NXF_VER=23.04.1`, or later. This version will use DSL2 as default.
+    This tutorial workshop requires `NXF_VER=23.10.0`, or later.
 
 Run `nextflow -version` again to confirm that the change has taken effect.

docs/basic_training/setup.pt.md

@@ -162,11 +162,11 @@ Os últimos lançamentos podem ser vistos no GitHub [aqui](https://github.com/ne
 Se você deseja usar uma versão específica do Nextflow, pode definir a variável `NXF_VER` conforme mostrado abaixo:
 
 ```bash
-export NXF_VER=23.04.1
+export NXF_VER=23.10.0
 ```
 
 !!! Note
 
-    Este treinamento requer `NXF_VER=23.04.1`, ou posterior. Esta versão usará a DSL2 como padrão.
+    Este treinamento requer `NXF_VER=23.10.0`, ou posterior. Esta versão usará a DSL2 como padrão.
 
 Execute `nextflow -version` novamente para confirmar que a alteração entrou em vigor.

nf-training/hello_py.nf

@@ -0,0 +1,41 @@
+#!/usr/bin/env nextflow
+
+params.greeting = 'Hello world!'
+greeting_ch = Channel.of(params.greeting)
+
+process SPLITLETTERS {
+    input:
+    val x
+
+    output:
+    path 'chunk_*'
+
+    """
+    #!/usr/bin/env python
+    x="$x"
+    for i, word in enumerate(x.split()):
+        with open(f"chunk_{i}", "w") as f:
+            f.write(word)
+    """
+}
+
+process CONVERTTOUPPER {
+    input:
+    path y
+
+    output:
+    stdout
+
+    """
+    #!/usr/bin/env python
+    with open("$y") as f:
+        print(f.read().upper())
+    """
+}
+
+workflow {
+    letters_ch = SPLITLETTERS(greeting_ch)
+    results_ch = CONVERTTOUPPER(letters_ch.flatten())
+    results_ch.view{ it }
+}
+