https://github.com/quiltdata/nf-quilt
https://github.com/quiltdata/nf-quilt
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/quiltdata/nf-quilt
- Owner: quiltdata
- License: gpl-3.0
- Created: 2022-10-13T22:22:03.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-03-23T22:25:58.000Z (about 1 year ago)
- Last Synced: 2025-03-23T23:26:48.409Z (about 1 year ago)
- Language: Groovy
- Size: 1.19 MB
- Stars: 9
- Watchers: 3
- Forks: 1
- Open Issues: 18
-
Metadata Files:
- Readme: README-DEV.md
- Changelog: CHANGELOG.md
- License: COPYING
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README
# Developer Documentation
## Using Pre-Release Versions
Occasionally we will release beta versions of the plugin that are not yet
available in the Nextflow plugin registry. You can help test these versions as
follows:
- Set the `NXF_PLUGINS_TEST_REPOSITORY` environment variable to the URL of the
plugin's metadata file
- Specify the plugin version in the `plugins` section of your `nextflow.config`
file
From the command-line, do, e.g.:
```bash
export LOG4J_DEBUG=true # for verbose logging
export VERSION=0.9.1
export NXF_PLUGINS_TEST_REPOSITORY=https://github.com/quiltdata/nf-quilt/releases/download/$(VERSION)/nf-quilt-$(VERSION)-meta.json
nextflow run main.nf -plugins nf-quilt@$(VERSION)
```
For Tower, you set the environment variables in the "Pre-run script".
## Using Development Versions
If you want to use edge versions of nf-quilt, you must run it with a development
version of `nextflow`. The simplest way to do that is to pull them both directly
from GitHub:
```bash
git clone https://github.com/nextflow.io/nextflow.git
git clone https://github.com/quiltdata/nf-quilt.git
cd ./nf-quilt
```
### Verifying Nextflow
If this is your first time using Nextflow, you may also need to install a recent
[version of Java](https://www.java.com/en/download/help/download_options.html)
for your platform. Nextflow itself will take care of all the other dependencies.
You can verify and compile Nextflow with:
```bash
make nextflow
```
## Running from Git
To quickly run `nf-quilt` from this GitHub repository:
```bash
# install and compiles dependencies, then test
make test-all
# create "test/hurdat" package on s3://$WRITE_BUCKET
make pkg-test WRITE_BUCKET=your-writeablebucket
```
This ensures you have properly installed Nextflow and configured your local
<--markdownlint-disable-next-line MD041-->
[AWS credentials](https://docs.aws.amazon.com/cli/latest/userguide/cli-configure-files.html).
You can also set WRITE_BUCKET and other parameters in a `.env` file in the
project root, and they will be automatically read by the Makefile.
### Running a Pipeline Locally
From inside the `nf-quilt` directory, call `./launch.sh` with a path to your
pipeline.
For example, with a standard `nf-core` pipeline like `sarek`:
```bash
./launch.sh run nf-core/sarek -profile test,docker -plugins nf-quilt --outdir "quilt+s3://bucket#package=nf-quilt/sarek"
```
Otherwise, replace `nf-core/sarek` with the local path to your pipeline's `.nf`
file (be sure to rename the `outdir` parameter if you use different convention).
For example:
```bash
./launch.sh run ./main.nf -profile standard -plugins $(PROJECT) --outdir "quilt+s3://bucket#package=test/hurdat"
```
There are standard Makefile targets for both `sarek` and `fetchngs` pipelines, which will test against the latest published versions of nf-quilt:
```bash
make sarek
make fetchngs
```
### Unit Testing
You can cleanly compile and run all unit tests with:
```bash
make check
```
To show the output of the tests, use:
```bash
make verify
```
To fast-fail on the first failing test, use:
```bash
make fast
```
## Publishing the Plugin for Others to Use
If your system is properly configured, use `make publish` to package, upload,
and publish the plugin.
Otherwise, follow these steps:
1. Create a file named `gradle.properties` in the user's home (NOT project)
directory containing the following attributes:
- `github_organization`: the GitHub organisation where the plugin repository
is hosted.
- `github_username`: The GitHub username granting access to the plugin
repository.
- `github_access_token`: The GitHub access token required to upload and
commit changes to the plugin repository.
- `github_commit_email`: The email address associated with your GitHub
account.
2. Use the following command to package and create a release for your plugin on
GitHub:
```bash
./gradlew :plugins:nf-quilt:upload
```
3. Fork the [nextflow-io/plugins](https://github.com/nextflow-io/plugins)
repository to one you can write to
4. Use the following command to publish your plugin to your fork:
```bash
./gradlew :plugins:publishIndex
```
5. Create a pull request to push your changes back to
[nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json)