Added nf-core template

.editorconfig

@@ -31,3 +31,30 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# These files are edited and tested upstream in gallvp/modules,subworkflows
+[/modules/gallvp/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+[/subworkflows/gallvp/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+# ignore perl
+[*.{pl,pm}]
+indent_size = unset
+
+# ignore drawio
+[*.drawio]
+indent_size = unset
+
+# ignore LICENSE
+[LICENSE]
+indent_size = unset

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# PlantandFoodResearch/genepal: Contributing Guidelines
+# plant-food-research-open/genepal: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving PlantandFoodResearch/genepal.
+Many thanks for taking an interest in improving plant-food-research-open/genepal.
 
-We try to manage the required tasks for PlantandFoodResearch/genepal using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for plant-food-research-open/genepal using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for PlantandFoodResearch/genepal, the standard workflow is as follows:
+If you'd like to write some code for plant-food-research-open/genepal, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [PlantandFoodResearch/genepal issues](https://github.com/PlantandFoodResearch/genepal/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [PlantandFoodResearch/genepal repository](https://github.com/PlantandFoodResearch/genepal) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [plant-food-research-open/genepal issues](https://github.com/plant-food-research-open/genepal/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [plant-food-research-open/genepal repository](https://github.com/plant-food-research-open/genepal) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Pipeline contribution conventions
 
-To make the PlantandFoodResearch/genepal code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the plant-food-research-open/genepal code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/PlantandFoodResearch/genepal/codespaces)
+- Open the repo in [Codespaces](https://github.com/plant-food-research-open/genepal/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -49,6 +49,6 @@ body:
 
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
 
-        * Version of PlantandFoodResearch/genepal _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of plant-food-research-open/genepal _(eg. 1.1, 1.5, 1.8.2)_
 
         "

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the PlantandFoodResearch/genepal pipeline
+description: Suggest an idea for the plant-food-research-open/genepal pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# PlantandFoodResearch/genepal pull request
+# plant-food-research-open/genepal pull request
 
-Many thanks for contributing to PlantandFoodResearch/genepal!
+Many thanks for contributing to plant-food-research-open/genepal!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/PlantandFoodResearch/genepal/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/plant-food-research-open/genepal/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/PlantandFoodResearch/genepal/tree/master/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/plant-food-research-open/genepal/tree/master/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/version_checks.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+config_version=$(sed -n "s/.*version.*= '\(.*\)'.*/\1/p" nextflow.config)
+
+# Check CHANGELOG version
+
+head -n 10 CHANGELOG.md | grep "## $config_version - " >/dev/null \
+    || (echo 'Failed to match CHANGELOG version'; exit 1)

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'PlantandFoodResearch/genepal'
+        if: github.repository == 'plant-food-research-open/genepal'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == PlantandFoodResearch/genepal ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == plant-food-research-open/genepal ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/ci.yml

@@ -18,14 +18,13 @@ concurrency:
 jobs:
   test:
     name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'PlantandFoodResearch/genepal') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'plant-food-research-open/genepal') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
           - "23.04.0"
-          - "latest-everything"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -39,8 +38,9 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run \
+            main.nf \
+            -profile docker \
+            -stub \
+            -params-file tests/stub/params.json

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'PlantandFoodResearch/genepal'
+      github.repository == 'plant-food-research-open/genepal'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/PlantandFoodResearch/genepal/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/plant-food-research-open/genepal/actions/runs/${{ github.run_id }}) for more details.

.gitignore

@@ -6,3 +6,6 @@ results/
 testing/
 testing*
 *.pyc
+
+*.stdout
+*.stderr

.nf-core.yml

@@ -22,6 +22,6 @@ lint:
 nf_core_version: 2.14.1
 repository_type: pipeline
 template:
-  prefix: PlantandFoodResearch
+  prefix: plant-food-research-open
   skip:
     - igenomes

.pre-commit-config.yaml

@@ -11,3 +11,13 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+  - repo: local
+    hooks:
+      - id: version_checks
+        name: Version checks
+        language: system
+        entry: >
+          .github/version_checks.sh
+        always_run: true
+        fail_fast: true
+        pass_filenames: false