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Merge pull request #86 from Daniel-VM/dev
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Merging template updates 2.9 and workflow update
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Daniel-VM authored Sep 20, 2023
2 parents d96132a + 5c6fbee commit ba415ef
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27 changes: 27 additions & 0 deletions .devcontainer/devcontainer.json
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{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",

// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
},

// 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"]
}
}
}
5 changes: 1 addition & 4 deletions .editorconfig
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Expand Up @@ -8,12 +8,9 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{yml,yaml}]
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2

[*.json]
insert_final_newline = unset

# These files are edited and tested upstream in nf-core/modules
[/modules/nf-core/**]
charset = unset
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3 changes: 3 additions & 0 deletions .gitattributes
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@@ -1 +1,4 @@
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
58 changes: 24 additions & 34 deletions .github/CONTRIBUTING.md
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Expand Up @@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)

If you'd like to write some code for nf-core/bacass, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [nf-core/bacass issues](https://github.com/nf-core/bacass/issues) to avoid duplicating work
* If there isn't one already, please create one so that others know you're working on this
1. Check that there isn't already an issue about your idea in the [nf-core/bacass issues](https://github.com/nf-core/bacass/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 [nf-core/bacass repository](https://github.com/nf-core/bacass) 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).
Expand Down Expand Up @@ -49,9 +48,9 @@ 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

Expand All @@ -68,16 +67,13 @@ If you wish to contribute a new step, please use the following coding standards:
1. Define the corresponding input channel into your new process from the expected previous process channel
2. Write the process block (see below).
3. Define the output channel if needed (see below).
4. Add any new flags/options to `nextflow.config` with a default (see below).
5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build`).
6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
7. Add sanity checks for all relevant parameters.
8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
9. Do local tests that the new code works properly and as expected.
10. Add a new test command in `.github/workflow/ci.yml`.
11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
4. Add any new parameters to `nextflow.config` with a default (see below).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
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`.

### Default values

Expand All @@ -95,34 +91,28 @@ 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_<process>`
* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`

### Software version reporting

If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.

Add to the script block of the process, something like the following:
### Images and figures

```bash
<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
```
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

or
## GitHub Codespaces

```bash
<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
```
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.

You then need to edit the script `bin/scrape_software_versions.py` to:
To get started:

1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
- Open the repo in [Codespaces](https://github.com/nf-core/bacass/codespaces)
- Tools installed
- nf-core
- Nextflow

### Images and figures
Devcontainer specs:

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
- [DevContainer config](.devcontainer/devcontainer.json)
63 changes: 0 additions & 63 deletions .github/ISSUE_TEMPLATE/bug_report.md

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50 changes: 50 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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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:
- [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [nf-core/bacass pipeline documentation](https://nf-co.re/bacass/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: 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
- 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/bacass _(eg. 1.1, 1.5, 1.8.2)_
1 change: 0 additions & 1 deletion .github/ISSUE_TEMPLATE/config.yml
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@@ -1,4 +1,3 @@
blank_issues_enabled: false
contact_links:
- name: Join nf-core
url: https://nf-co.re/join
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32 changes: 0 additions & 32 deletions .github/ISSUE_TEMPLATE/feature_request.md

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11 changes: 11 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.yml
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name: Feature request
description: Suggest an idea for the nf-core/bacass 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
7 changes: 3 additions & 4 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -10,16 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)
-->
<!-- markdownlint-disable ul-indent -->

## 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/bacass/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/bacass _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/bacass/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/bacass _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`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
- [ ] `CHANGELOG.md` is updated.
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16 changes: 11 additions & 5 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,20 +14,26 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@master
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters

with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
pipeline: ${{ github.repository }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}"
}
profiles: '[ "test_full", "aws_tower" ]'
profiles: test_full

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
17 changes: 11 additions & 6 deletions .github/workflows/awstest.yml
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Expand Up @@ -10,19 +10,24 @@ jobs:
if: github.repository == 'nf-core/bacass'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: nf-core/tower-action@master

uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
pipeline: ${{ github.repository }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/bacass/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-${{ github.sha }}"
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/bacass/results-test-${{ github.sha }}"
}
profiles: '[ "test", "aws_tower" ]'
profiles: test

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: |
tower_action_*.log
tower_action_*.json
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