Initial commit

.github/workflows/template.yml

@@ -0,0 +1,75 @@
+name: Execute template to populate repository
+
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  setup-repo:
+    if: ${{ github.repository != 'Sydney-Informatics-Hub/template-nf' }}
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          ref: ${{ github.head_ref }}
+
+      - name: Install cookiecutter
+        run: pip3 install cookiecutter
+
+      - uses: actions/github-script@v4
+        id: fetch-repo-and-user-details
+        with:
+          script: |
+            const query = `query($owner:String!, $name:String!) {
+              repository(owner:$owner, name:$name) {
+                name
+                description
+                owner {
+                  login
+                  ... on User {
+                    name
+                  }
+                  ... on Organization {
+                    name
+                  }
+                }
+              }
+            }`;
+            const variables = {
+              owner: context.repo.owner,
+              name: context.repo.repo
+            }
+            const result = await github.graphql(query, variables)
+            return result
+
+      - name: Build out template 
+        env:
+          INFO: ${{ steps.fetch-repo-and-user-details.outputs.result }}
+        run: |
+          export REPO_NAME=$(echo $INFO | jq -r '.repository.name')
+          # Run cookiecutter
+          pushd /tmp
+          cookiecutter gh:Sydney-Informatics-Hub/Nextflow_DSL2_template --no-input \
+            app_name=$REPO_NAME \
+            description="$(echo $INFO | jq -r .repository.description)" \
+            github_username="$(echo $INFO | jq -r .repository.owner.login)" \
+            author_name="$(echo $INFO | jq -r .repository.owner.name)"
+          popd
+          # Delete the .github directory and README, they're not needed anymore
+          rm -rf .github/ 
+          rm -rf Images/
+          rm -rf README.md
+          shopt -s dotglob
+          # Move template content to root, ensure hidden and README are replaced
+          rsync -a /tmp/$REPO_NAME/ .
+
+      - name: Force push changes to main
+        uses: stefanzweifel/git-auto-commit-action@v4
+        with:
+          commit_message: "Build skeleton template"
+          push_options: "--force"

README.md

@@ -0,0 +1,62 @@
+# template-nf
+
+This is a Nextflow workflow template generator. This template is under development, with further features and improved documentation to be added. 
+
+## **Why use this template?** 
+
+[Nextflow](https://www.nextflow.io/) is open source and scalable workflow management software, developed for bioinformatics. It enables the development and execution of integrated, reproducible workflows consisting of multiple processes, various environment management systems, scripting languages, and software packages. 
+
+Given Nextflow's extensive capabilities, there are many ways to structure your workflows. We developed this template to aid beginners in learning how to develop best practice Nextflow workflows. Here, we've prioritised modularity, portability, and flexibility.  
+
+## **Who is this template for?** 
+
+The DSL2 workflow template is suitable for:
+
+* Nextflow newcomers looking for a low barrier to entry, structured starting point, and guidance.
+* Custom workflow developers looking for a simple scaffold which can be extended and modified as needed.
+* Collaborative teams looking for a standard and consistent workflow code base structure.
+* Scalable workflow developers looking for a scalable and reproducible solution for their data analysis and processing needs.
+
+It is not suitable for:
+
+* Those wishing to create and contribute to public nf-core workflows, as it is not nf-core compatible.
+* Those creating simple or single-task workflows with only a few tasks and minimal complexity.
+* Those with no previous command-line and bash experience.
+
+## **How to use the template?** 
+
+Once you create a new repository using this template, a GitHub Action workflow will automatically be deployed. This workflow will populate your new repository with the skeleton template directory. To create a new repository: 
+
+1. On this page, select the 'Use this template' button, and select the green 'Create new repository' button: 
+
+![](./Images/01_usetemplate.png)
+
+2. You'll be taken to a new page where you can configure your new repository. Ensure the 'Include all branches' box is unticked, give your workflow a name, a description (optional), and select whether it should be public or private. Then hit the green 'Create repository' button: 
+
+![](./Images/02_newrepo.png)
+
+3. You'll be taken to your new repository page. It will appear like nothing has happened, take note of the brown dot on the top of the code tab/section on this page. This indicates that the GitHub Action is working, if you select it you can observe its progress as it repopulates your repository with the template. It may take a few seconds to run: 
+
+![](./Images/03_action.png)
+
+4. Once this brown dot is replaced by a green tick the Action has successfully completed and your repository will be populated with the Nextflow template code base. You may need to refresh your page to observe these changes: 
+
+![](./Images/04_template.png)
+
+5. Once your repository has been populated with the template code base, you can open it on your CLI environment and develop your workflow. For example: 
+
+```
+git clone https://github.com/georgiesamaha/myWorkflow-nf.git
+```
+
+### [User guide](https://sydney-informatics-hub.github.io/Nextflow_DSL2_template_guide/) 
+
+Please see our [documentation](https://sydney-informatics-hub.github.io/Nextflow_DSL2_template_guide/) for instructions on how to use the template code base to build your workflow.
+
+### Install Nextflow
+
+Depending on the system you're working on there are a few options for installing and running Nextflow including software management tools like bioconda and Singularity. See [here](https://www.nextflow.io/docs/latest/getstarted.html#installation) for installation instructions. Once you have installed Nextflow, you can configure it to run on your system if needed. 
+
+## **Acknowledgements** 
+
+The work presented here was developed by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney and the Australian BioCommons 'Bring Your Own Data' Platforms Project which is enabled by NCRIS via ARDC and Bioplatforms Australia.