Updated info in .github directory

.github/CONTRIBUTING.md

@@ -1,17 +1,17 @@
 # phac-nml/iridanextexample: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving phac-nml/iridanextexample.
+Many thanks for taking an interest in improving phac-nml/fetchdatairidanext.
 
-We try to manage the required tasks for phac-nml/iridanextexample using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for phac-nml/fetchdatairidanext using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 ## Contribution workflow
 
-If you'd like to write some code for phac-nml/iridanextexample, the standard workflow is as follows:
+If you'd like to write some code for phac-nml/fetchdatairidanext, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [phac-nml/iridanextexample issues](https://github.com/phac-nml/iridanextexample/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 [phac-nml/iridanextexample repository](https://github.com/phac-nml/iridanextexample) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [phac-nml/fetchdatairidanext issues](https://github.com/phac-nml/fetchdatairidanext/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 [phac-nml/fetchdatairidanext repository](https://github.com/phac-nml/fetchdatairidanext) 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
@@ -27,7 +27,7 @@ There are typically two types of tests that run:
 
 ### Lint tests
 
-`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to.
+`phac-nml` has a [set of guidelines](https://github.com/phac-nml/pipeline-standards) which all pipelines must adhere to. These are a subset of the [nf-core set of guidelines](https://nf-co.re/developers/guidelines).
 To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command.
 
 If any failures or warnings are encountered, please follow the listed URL for more documentation.
@@ -49,11 +49,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [phac-nml/iridanextexample documentation](https://github.com/phac-nml/iridanextexample/).
+For further information/help, please consult the [phac-nml/fetchdatairidanext documentation](https://github.com/phac-nml/fetchdatairidanext/).
 
 ## Pipeline contribution conventions
 
-To make the phac-nml/iridanextexample 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 phac-nml/fetchdatairidanext 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
 
@@ -67,8 +67,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+9. Add a description of the output files to `docs/output.md`.
 
 ### Default values
 
@@ -96,18 +95,3 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-
-## GitHub Codespaces
-
-This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
-
-To get started:
-
-- Open the repo in [Codespaces](https://github.com/phac-nml/iridanextexample/codespaces)
-- Tools installed
-  - nf-core
-  - Nextflow
-
-Devcontainer specs:
-
-- [DevContainer config](.devcontainer/devcontainer.json)

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,4 @@
 contact_links:
   - name: "GitHub"
-    url: https://github.com/phac-nml/iridanextexample
+    url: https://github.com/phac-nml/fetchdatairidanext
     about: The GitHub page for development.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the phac-nml/iridanextexample pipeline
+description: Suggest an idea for the phac-nml/fetchdatairidanext pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,21 +1,21 @@
 <!--
-# phac-nml/iridanextexample pull request
+# phac-nml/fetchdatairidanext pull request
 
-Many thanks for contributing to phac-nml/iridanextexample!
+Many thanks for contributing to phac-nml/fetchdatairidanext!
 
 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/phac-nml/iridanextexample/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/phac-nml/fetchdatairidanext/tree/main/.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/phac-nml/iridanextexample/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/phac-nml/fetchdatairidanext/tree/main/.github/CONTRIBUTING.md)
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/branch.yml

@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the phac-nml repo main branch are only ok if coming from the phac-nml repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'phac-nml/iridanextexample'
+        if: github.repository == 'phac-nml/fetchdatairidanext'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/iridanextexample ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == phac-nml/fetchdatairidanext ]] && [[ $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

@@ -19,7 +19,7 @@ jobs:
   test:
     name: Run pipeline with test data
     # Only run on push if this is the phac-nml dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/iridanextexample') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'phac-nml/fetchdatairidanext') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix: