add pixi env

.devcontainer/Dockerfile

@@ -0,0 +1,13 @@
+FROM mcr.microsoft.com/devcontainers/base:jammy
+
+ARG PIXI_VERSION=v0.71.0
+
+RUN curl -L -o /usr/local/bin/pixi -fsSL --compressed "https://github.com/prefix-dev/pixi/releases/download/${PIXI_VERSION}/pixi-$(uname -m)-unknown-linux-musl" \
+    && chmod +x /usr/local/bin/pixi \
+    && pixi info
+
+# set some user and workdir settings to work nicely with vscode
+USER vscode
+WORKDIR /home/vscode
+
+RUN echo 'eval "$(pixi completion -s bash)"' >> /home/vscode/.bashrc

.devcontainer/devcontainer.json

@@ -1,21 +1,30 @@
 {
     "name": "nfcore-modules",
-    "image": "nfcore/devcontainer:dev",
-
+    "build": {
+        "dockerfile": "Dockerfile",
+        "context": ".."
+    },
     "remoteEnv": {
         // Workspace path on the host for mounting with docker-outside-of-docker
         "LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}",
         "DOCKER_API_VERSION": "1.43"
     },
-
-    "onCreateCommand": "./.devcontainer/setup.sh",
-
     "remoteUser": "root",
     "privileged": true,
-
     "hostRequirements": {
         "cpus": 4,
         "memory": "16gb",
         "storage": "32gb"
-    }
+    },
+    "customizations": {
+        "vscode": {
+            "settings": {},
+            "extensions": ["ms-python.python"]
+        }
+    },
+    "features": {
+        "ghcr.io/devcontainers/features/docker-in-docker:2": {}
+    },
+    "mounts": ["source=${localWorkspaceFolderBasename}-pixi,target=${containerWorkspaceFolder}/.pixi,type=volume"],
+    "postCreateCommand": "./.devcontainer/setup.sh"
 }

.devcontainer/setup.sh

@@ -5,8 +5,7 @@ echo "export PROMPT_DIRTRIM=2" >> $HOME/.bashrc
 echo "export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '" >> $HOME/.bashrc
 export PS1='\[\e[3;36m\]\w ->\[\e[0m\\] '
 
-# Update Nextflow
-nextflow self-update
+sudo chown vscode .pixi && pixi shell
 
 # Install prek hooks
 pip install prek

.gitattributes

@@ -1,3 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
 *.nf.test.snap linguist-language=json
+# SCM syntax highlighting & preventing 3-way merges
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

.gitignore

@@ -15,3 +15,7 @@ test_output/
 tests/data/
 work/
 .github/CODEOWNERS-tmp
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+pixi.lock

README.md

@@ -136,6 +136,10 @@ If you wish to contribute a new module, please see the documentation on the [nf-
 
 > Please be kind to our code reviewers and submit one pull request per module :)
 
+### Dependency management
+
+All required dependencies for module development are listed in `pixi.toml` and can be installed with `pixi install`. Please see the [pixi documentation](https://nf-co.re/developers/pixi) for more information.
+
 ## Help
 
 For further information or help, don't hesitate to get in touch on [Slack `#modules` channel](https://nfcore.slack.com/channels/modules) (you can join with [this invite](https://nf-co.re/join/slack)).

pixi.toml

@@ -0,0 +1,17 @@
+[workspace]
+authors = ["nf-core core team <core@nf-co.re>"]
+channels = ["conda-forge", "bioconda"]
+name = "modules"
+platforms = ["osx-arm64", "linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+prek = ">=0.4.5,<0.5"
+python = ">=3.14.6,<3.15"
+nextflow = ">=26.4.4,<27"
+nf-test = ">=0.9.5,<0.10"
+
+[pypi-dependencies]
+nf-core = { git = "https://github.com/nf-core/tools.git", tag = "dev" }