From 75da2a3c8c92783b1f6f827ccf87f7e33a891651 Mon Sep 17 00:00:00 2001 From: Woo Jung Date: Tue, 13 Feb 2024 13:09:06 -0600 Subject: [PATCH] updates to fix prettier linting --- .devcontainer/devcontainer.json | 6 +- .github/.dockstore.yml | 6 +- .github/CONTRIBUTING.md | 20 +-- .github/ISSUE_TEMPLATE/bug_report.yml | 80 ++++++------ .github/ISSUE_TEMPLATE/config.yml | 12 +- .github/ISSUE_TEMPLATE/feature_request.yml | 14 +- .github/PULL_REQUEST_TEMPLATE.md | 22 ++-- .github/workflows/branch.yml | 76 +++++------ .github/workflows/ci.yml | 62 ++++----- .github/workflows/linting.yml | 104 +++++++-------- .github/workflows/linting_comment.yml | 38 +++--- CODE_OF_CONDUCT.md | 122 +++++++++--------- assets/methods_description_template.yml | 38 +++--- assets/multiqc_config.yml | 18 +-- docs/README.md | 8 +- .../custom/dumpsoftwareversions/meta.yml | 56 ++++---- .../dumpsoftwareversions/tests/tags.yml | 2 +- modules/nf-core/fastqc/environment.yml | 8 +- modules/nf-core/fastqc/meta.yml | 98 +++++++------- modules/nf-core/fastqc/tests/tags.yml | 2 +- modules/nf-core/multiqc/tests/tags.yml | 2 +- tower.yml | 8 +- 22 files changed, 403 insertions(+), 399 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe..6af5b50 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -22,7 +22,11 @@ }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + "extensions": [ + "ms-python.python", + "ms-python.vscode-pylance", + "nf-core.nf-core-extensionpack" + ] } } } diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml index 191fabd..b9d3387 100644 --- a/.github/.dockstore.yml +++ b/.github/.dockstore.yml @@ -1,6 +1,6 @@ # Dockstore config version, not pipeline version version: 1.2 workflows: - - subclass: nfl - primaryDescriptorPath: /nextflow.config - publish: True + - subclass: nfl + primaryDescriptorPath: /nextflow.config + publish: True diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 2c80c00..9a480ec 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -53,9 +53,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. -- Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- On your own fork, make a new branch `patch` based on `upstream/master`. +- Fix the bug, and bump version (X.Y.Z+1). +- A PR should be made on `master` from patch to directly this particular bug. ## Getting help @@ -96,8 +96,8 @@ The process resources can be passed on to the tool dynamically within the proces Please use the following naming schemes, to make it easy to understand what is going where. -- initial process channel: `ch_output_from_` -- intermediate and terminal channels: `ch__for_` +- initial process channel: `ch_output_from_` +- intermediate and terminal channels: `ch__for_` ### Nextflow version bumping @@ -113,11 +113,11 @@ This repo includes a devcontainer configuration which will create a GitHub Codes To get started: -- Open the repo in [Codespaces](https://github.com/nf-core/omicsgenetraitassociation/codespaces) -- Tools installed - - nf-core - - Nextflow +- Open the repo in [Codespaces](https://github.com/nf-core/omicsgenetraitassociation/codespaces) +- Tools installed + - nf-core + - Nextflow Devcontainer specs: -- [DevContainer config](.devcontainer/devcontainer.json) +- [DevContainer config](.devcontainer/devcontainer.json) diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index 6c6f783..4714694 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -2,49 +2,49 @@ name: Bug report description: Report something that is broken or incorrect labels: bug body: - - type: markdown - attributes: - value: | - Before you post this issue, please check the documentation: + - type: markdown + attributes: + value: | + Before you post this issue, please check the documentation: - - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - - [nf-core/omicsgenetraitassociation pipeline documentation](https://nf-co.re/omicsgenetraitassociation/usage) + - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) + - [nf-core/omicsgenetraitassociation pipeline documentation](https://nf-co.re/omicsgenetraitassociation/usage) - - type: textarea - id: description - attributes: - label: Description of the bug - description: A clear and concise description of what the bug is. - validations: - required: true + - type: textarea + id: description + attributes: + label: Description of the bug + description: A clear and concise description of what the bug is. + validations: + required: true - - type: textarea - id: command_used - attributes: - label: Command used and terminal output - description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. - render: console - placeholder: | - $ nextflow run ... + - type: textarea + id: command_used + attributes: + label: Command used and terminal output + description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. + render: console + placeholder: | + $ nextflow run ... - Some output where something broke + Some output where something broke - - type: textarea - id: files - attributes: - label: Relevant files - description: | - Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. - Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. + - type: textarea + id: files + attributes: + label: Relevant files + description: | + Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. + Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. - - type: textarea - id: system - attributes: - label: System information - description: | - * Nextflow version _(eg. 23.04.0)_ - * Hardware _(eg. HPC, Desktop, Cloud)_ - * Executor _(eg. slurm, local, awsbatch)_ - * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ - * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of nf-core/omicsgenetraitassociation _(eg. 1.1, 1.5, 1.8.2)_ + - type: textarea + id: system + attributes: + label: System information + description: | + * Nextflow version _(eg. 23.04.0)_ + * Hardware _(eg. HPC, Desktop, Cloud)_ + * Executor _(eg. slurm, local, awsbatch)_ + * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_ + * OS _(eg. CentOS Linux, macOS, Linux Mint)_ + * Version of nf-core/omicsgenetraitassociation _(eg. 1.1, 1.5, 1.8.2)_ diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 80016e8..f8b33e4 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1,7 +1,7 @@ contact_links: - - name: Join nf-core - url: https://nf-co.re/join - about: Please join the nf-core community here - - name: "Slack #omicsgenetraitassociation channel" - url: https://nfcore.slack.com/channels/omicsgenetraitassociation - about: Discussion about the nf-core/omicsgenetraitassociation pipeline + - name: Join nf-core + url: https://nf-co.re/join + about: Please join the nf-core community here + - name: "Slack #omicsgenetraitassociation channel" + url: https://nfcore.slack.com/channels/omicsgenetraitassociation + about: Discussion about the nf-core/omicsgenetraitassociation pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index 86c7556..b2a12a1 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -2,10 +2,10 @@ name: Feature request description: Suggest an idea for the nf-core/omicsgenetraitassociation pipeline labels: enhancement body: - - type: textarea - id: description - attributes: - label: Description of feature - description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. - validations: - required: true + - type: textarea + id: description + attributes: + label: Description of feature + description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. + validations: + required: true diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 3c7c096..15b4759 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -13,14 +13,14 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/omic ## 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/nf-core/omicsgenetraitassociation/tree/master/.github/CONTRIBUTING.md) -- [ ] If necessary, also make a PR on the nf-core/omicsgenetraitassociation _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). -- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). -- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). -- [ ] Usage Documentation in `docs/usage.md` is updated. -- [ ] Output Documentation in `docs/output.md` is updated. -- [ ] `CHANGELOG.md` is updated. -- [ ] `README.md` is updated (including new tool citations and authors/contributors). +- [ ] 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/nf-core/omicsgenetraitassociation/tree/master/.github/CONTRIBUTING.md) +- [ ] If necessary, also make a PR on the nf-core/omicsgenetraitassociation _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. +- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). +- [ ] Usage Documentation in `docs/usage.md` is updated. +- [ ] Output Documentation in `docs/output.md` is updated. +- [ ] `CHANGELOG.md` is updated. +- [ ] `README.md` is updated (including new tool citations and authors/contributors). diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 4da88b6..2788e24 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -2,43 +2,43 @@ name: nf-core branch protection # This workflow is triggered on PRs to master branch on the repository # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` on: - pull_request_target: - branches: [master] + pull_request_target: + branches: [master] jobs: - test: - runs-on: ubuntu-latest - 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 == 'nf-core/omicsgenetraitassociation' - run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/omicsgenetraitassociation ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] - - # If the above check failed, post a comment on the PR explaining the failure - # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets - - name: Post PR comment - if: failure() - uses: mshick/add-pr-comment@v2 - with: - message: | - ## This PR is against the `master` branch :x: - - * Do not close this PR - * Click _Edit_ and change the `base` to `dev` - * This CI test will remain failed until you push a new commit - - --- - - Hi @${{ github.event.pull_request.user.login }}, - - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. - - You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. - Note that even after this, the test will continue to show as failing until you push a new commit. - - Thanks again for your contribution! - repo-token: ${{ secrets.GITHUB_TOKEN }} - allow-repeats: false + test: + runs-on: ubuntu-latest + 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 == 'nf-core/omicsgenetraitassociation' + run: | + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/omicsgenetraitassociation ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + + # If the above check failed, post a comment on the PR explaining the failure + # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v2 + with: + message: | + ## This PR is against the `master` branch :x: + + * Do not close this PR + * Click _Edit_ and change the `base` to `dev` + * This CI test will remain failed until you push a new commit + + --- + + Hi @${{ github.event.pull_request.user.login }}, + + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. + The `master` branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + + You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. + Note that even after this, the test will continue to show as failing until you push a new commit. + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 0b68d01..1b48caa 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,42 +1,42 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - push: - branches: - - dev - pull_request: - release: - types: [published] + push: + branches: + - dev + pull_request: + release: + types: [published] env: - NXF_ANSI_LOG: false + NXF_ANSI_LOG: false concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true + group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" + cancel-in-progress: true jobs: - test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/omicsgenetraitassociation') }}" - runs-on: ubuntu-latest - strategy: - matrix: - NXF_VER: - - "23.04.0" - - "latest-everything" - steps: - - name: Check out pipeline code - uses: actions/checkout@v4 + test: + name: Run pipeline with test data + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/omicsgenetraitassociation') }}" + runs-on: ubuntu-latest + strategy: + matrix: + NXF_VER: + - "23.04.0" + - "latest-everything" + steps: + - name: Check out pipeline code + uses: actions/checkout@v4 - - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 - with: - version: "${{ matrix.NXF_VER }}" + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - - name: Run pipeline with test data - # 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 + - name: Run pipeline with test data + # 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 diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 81cd098..06215b5 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -3,67 +3,67 @@ name: nf-core linting # It runs the `nf-core lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: - push: - branches: - - dev - pull_request: - release: - types: [published] + push: + branches: + - dev + pull_request: + release: + types: [published] jobs: - pre-commit: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 - - name: Set up Python 3.11 - uses: actions/setup-python@v5 - with: - python-version: 3.11 - cache: "pip" + - name: Set up Python 3.11 + uses: actions/setup-python@v5 + with: + python-version: 3.11 + cache: "pip" - - name: Install pre-commit - run: pip install pre-commit + - name: Install pre-commit + run: pip install pre-commit - - name: Run pre-commit - run: pre-commit run --all-files + - name: Run pre-commit + run: pre-commit run --all-files - nf-core: - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v4 + nf-core: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@v4 - - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 - - uses: actions/setup-python@v5 - with: - python-version: "3.11" - architecture: "x64" + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + architecture: "x64" - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install nf-core + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install nf-core - - name: Run nf-core lint - env: - GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + - name: Run nf-core lint + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Save PR number - if: ${{ always() }} - run: echo ${{ github.event.pull_request.number }} > PR_number.txt + - name: Save PR number + if: ${{ always() }} + run: echo ${{ github.event.pull_request.number }} > PR_number.txt - - name: Upload linting log file artifact - if: ${{ always() }} - uses: actions/upload-artifact@v4 - with: - name: linting-logs - path: | - lint_log.txt - lint_results.md - PR_number.txt + - name: Upload linting log file artifact + if: ${{ always() }} + uses: actions/upload-artifact@v4 + with: + name: linting-logs + path: | + lint_log.txt + lint_results.md + PR_number.txt diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 147bcd1..e433ebd 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -3,26 +3,26 @@ name: nf-core linting comment # It posts an automated comment to the PR, even if the PR is coming from a fork on: - workflow_run: - workflows: ["nf-core linting"] + workflow_run: + workflows: ["nf-core linting"] jobs: - test: - runs-on: ubuntu-latest - steps: - - name: Download lint results - uses: dawidd6/action-download-artifact@v3 - with: - workflow: linting.yml - workflow_conclusion: completed + test: + runs-on: ubuntu-latest + steps: + - name: Download lint results + uses: dawidd6/action-download-artifact@v3 + with: + workflow: linting.yml + workflow_conclusion: completed - - name: Get PR number - id: pr_number - run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT + - name: Get PR number + id: pr_number + run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT - - name: Post PR comment - uses: marocchino/sticky-pull-request-comment@v2 - with: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - number: ${{ steps.pr_number.outputs.pr_number }} - path: linting-logs/lint_results.md + - name: Post PR comment + uses: marocchino/sticky-pull-request-comment@v2 + with: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + number: ${{ steps.pr_number.outputs.pr_number }} + path: linting-logs/lint_results.md diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index c089ec7..ff18271 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -4,21 +4,21 @@ In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: -- Age -- Ability -- Body size -- Caste -- Familial status -- Gender identity and expression -- Geographical location -- Level of experience -- Nationality and national origins -- Native language -- Neurodiversity -- Race or ethnicity -- Religion -- Sexual identity and orientation -- Socioeconomic status +- Age +- Ability +- Body size +- Caste +- Familial status +- Gender identity and expression +- Geographical location +- Level of experience +- Nationality and national origins +- Native language +- Neurodiversity +- Race or ethnicity +- Religion +- Sexual identity and orientation +- Socioeconomic status Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance. @@ -54,38 +54,38 @@ Members of the core team or the Safety Team who violate the CoC will be required Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): -- Communicating with an official project email address. -- Communicating with community members within the nf-core Slack channel. -- Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. -- Representing nf-core on social media. This includes both official and personal accounts. +- Communicating with an official project email address. +- Communicating with community members within the nf-core Slack channel. +- Participating in hackathons organised by nf-core (both online and in-person events). +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. +- Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): -- Ask for consent before sharing another community member’s personal information (including photographs) on social media. -- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) -- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) -- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) -- Focus on what is best for the team and the community. (When in doubt, ask) -- Accept feedback, yet be unafraid to question, deliberate, and learn. -- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) -- Take breaks when you feel like you need them. -- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) +- Ask for consent before sharing another community member’s personal information (including photographs) on social media. +- Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) +- Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) +- Focus on what is best for the team and the community. (When in doubt, ask) +- Accept feedback, yet be unafraid to question, deliberate, and learn. +- Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) +- Take breaks when you feel like you need them. +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: -- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. -- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. -- Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. +- Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. +- “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. +- Spamming or trolling of individuals on social media. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling @@ -105,14 +105,14 @@ All reports will be handled with the utmost discretion and confidentiality. You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: -- Your contact information. -- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. -- The behaviour that was in violation and the circumstances surrounding the incident. -- The approximate time of the behaviour (if different than the time the report was made). -- Other people involved in the incident, if applicable. -- If you believe the incident is ongoing. -- If there is a publicly available record (e.g. mailing list record, a screenshot). -- Any additional information. +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. After you file a report, one or more members of our Safety Team will contact you to follow up on your report. @@ -144,39 +144,39 @@ We will not name harassment victims, beyond discussions between the safety offic Actions taken by the nf-core’s Safety Team may include, but are not limited to: -- Asking anyone to stop a behaviour. -- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. -- Removing access to the gather.town and Slack, either temporarily or permanently. -- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. -- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. -- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. -- No action. +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements -- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4) -- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition) -- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/) -- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla) +- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4) +- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition) +- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/) +- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla) ## Changelog ### v1.4 - February 8th, 2022 -- Included a new member of the Safety Team. Corrected a typographical error in the text. +- Included a new member of the Safety Team. Corrected a typographical error in the text. ### v1.3 - December 10th, 2021 -- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. ### v1.2 - November 12th, 2021 -- Removed information specific to reporting CoC violations at the Hackathon in October 2021. +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. ### v1.1 - October 14th, 2021 -- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. ### v1.0 - March 15th, 2021 -- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. +- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 22f8da5..dddc0a0 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -6,24 +6,24 @@ plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: | -

Methods

-

Data was processed using nf-core/omicsgenetraitassociation v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

-

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

- 
${workflow.commandLine}
-

${tool_citations}

-

References

-
    -
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • -
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • -
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • -
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • - ${tool_bibliography} -
-
-
Notes:
+

Methods

+

Data was processed using nf-core/omicsgenetraitassociation v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

+

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

+ 
${workflow.commandLine}
+

${tool_citations}

+

References

    - ${nodoi_text} -
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • -
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • +
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
    • +
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
    • +
  • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
    • +
  • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
    • + ${tool_bibliography}
-
+
+
Notes:
+
    + ${nodoi_text} +
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • +
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • +
+
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 516fbb5..b22135d 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,13 +1,13 @@ report_comment: > - This report has been generated by the nf-core/omicsgenetraitassociation - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/omicsgenetraitassociation + analysis pipeline. For information about how to interpret these results, please see the + documentation. report_section_order: - "nf-core-omicsgenetraitassociation-methods-description": - order: -1000 - software_versions: - order: -1001 - "nf-core-omicsgenetraitassociation-summary": - order: -1002 + "nf-core-omicsgenetraitassociation-methods-description": + order: -1000 + software_versions: + order: -1001 + "nf-core-omicsgenetraitassociation-summary": + order: -1002 export_plots: true diff --git a/docs/README.md b/docs/README.md index f69f875..b2af6e5 100644 --- a/docs/README.md +++ b/docs/README.md @@ -2,9 +2,9 @@ The nf-core/omicsgenetraitassociation documentation is split into the following pages: -- [Usage](usage.md) - - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. -- [Output](output.md) - - An overview of the different results produced by the pipeline and how to interpret them. +- [Usage](usage.md) + - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. +- [Output](output.md) + - An overview of the different results produced by the pipeline and how to interpret them. You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 5f15a5f..ea89d55 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -2,36 +2,36 @@ name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: - - custom - - dump - - version + - custom + - dump + - version tools: - - custom: - description: Custom module used to dump software versions within the nf-core pipeline template - homepage: https://github.com/nf-core/tools - documentation: https://github.com/nf-core/tools - licence: ["MIT"] + - custom: + description: Custom module used to dump software versions within the nf-core pipeline template + homepage: https://github.com/nf-core/tools + documentation: https://github.com/nf-core/tools + licence: ["MIT"] input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" + - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" output: - - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" - - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" + - mqc_yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" + - "@drpatelh" + - "@grst" maintainers: - - "@drpatelh" - - "@grst" + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml index 405aa24..12c9030 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -1,2 +1,2 @@ custom/dumpsoftwareversions: - - modules/nf-core/custom/dumpsoftwareversions/** + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38..0c6458a 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,7 @@ name: fastqc channels: - - conda-forge - - bioconda - - defaults + - conda-forge + - bioconda + - defaults dependencies: - - bioconda::fastqc=0.12.1 + - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e..6bada9f 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -1,57 +1,57 @@ name: fastqc description: Run FastQC on sequenced reads keywords: - - quality control - - qc - - adapters - - fastq + - quality control + - qc + - adapters + - fastq tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml index 7834294..da7a9d6 100644 --- a/modules/nf-core/fastqc/tests/tags.yml +++ b/modules/nf-core/fastqc/tests/tags.yml @@ -1,2 +1,2 @@ fastqc: - - modules/nf-core/fastqc/** + - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml index bea6c0d..788f3e4 100644 --- a/modules/nf-core/multiqc/tests/tags.yml +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -1,2 +1,2 @@ multiqc: - - modules/nf-core/multiqc/** + - modules/nf-core/multiqc/** diff --git a/tower.yml b/tower.yml index 787aedf..8a2441d 100644 --- a/tower.yml +++ b/tower.yml @@ -1,5 +1,5 @@ reports: - multiqc_report.html: - display: "MultiQC HTML report" - samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" + multiqc_report.html: + display: "MultiQC HTML report" + samplesheet.csv: + display: "Auto-created samplesheet with collated metadata and FASTQ paths"