diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index aecbd6e..e9013a8 100644 --- a/.github/CONTRIBUTING.md +++ b/.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 ` 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) diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index f0c034e..2a8df94 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.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. diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index e67ccaa..0204616 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.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 diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 63aed5f..146c253 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,21 +1,21 @@ ## 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 `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index d4ad0e4..d72ca17 100644 --- a/.github/workflows/branch.yml +++ b/.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" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 03e1016..745d17e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: test: name: Run pipeline with test data # Only run on push if this is the phac-nml dev branch (merged PRs) - if: "${{ 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: