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Nextflow, not NextFlow (#160)
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Because I'm a pedant, sorry.
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ewels authored Jan 10, 2024
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -87,12 +87,12 @@ Beta release (not yet on nextflow-io/plugins)

- Alpha: Call Benchling API after publishing package
- accept "?commit_message=text+string&readme=GString" in Quilt+ URI
- Support NextFlow 23+
- Support Nextflow 23+

## [0.3.3] 2023-03-08

- Fail gracefully on `quilt3` errors
- Detailed NextFlow Tower instructions
- Detailed Nextflow Tower instructions
- Call `quilt3` during integration tests
- Add full Quilt+ URL support, including metadata in query string

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20 changes: 10 additions & 10 deletions README.md
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# nf-quilt

NextFlow plugin for reading and writing Quilt packages as a FileSystem
Nextflow plugin for reading and writing Quilt packages as a FileSystem

[`nf-quilt`](https://github.com/quiltdata/nf-quilt) (v0.3.2 or later) is a NextFlow [plugin](https://www.nextflow.io/docs/latest/plugins.html)
[`nf-quilt`](https://github.com/quiltdata/nf-quilt) (v0.3.2 or later) is a Nextflow [plugin](https://www.nextflow.io/docs/latest/plugins.html)
developed by [Quilt Data](https://quiltdata.com/) that enables you read and write directly
to Quilt packages using `quilt+s3` URIs wherever your NextFlow pipeline currently use `s3` URIs.
to Quilt packages using `quilt+s3` URIs wherever your Nextflow pipeline currently use `s3` URIs.

Inspired by the original [`nf-quilt`](https://github.com/nextflow-io/nf-quilt) plugin (v0.2.0) developed by Seqera labs.

Expand All @@ -13,7 +13,7 @@ Inspired by the original [`nf-quilt`](https://github.com/nextflow-io/nf-quilt) p
This plugin allows your existing pipelines, without modification,
to read and write versioned Quilt packages stored on Amazon S3.

Use the following three steps to configure NextFlow Tower or your command-line environment.
Use the following three steps to configure Nextflow Tower or your command-line environment.
[Note: versions 0.7.0 and later no longer require the `quilt3` Python client.]

1. Enable the `nf-quilt` plugin
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1. Optional: use a pre-release plugin

If a plugin is not yet available in the NextFlow plugin registry, you can use a pre-release version.
If a plugin is not yet available in the Nextflow plugin registry, you can use a pre-release version.
From the command-line, do, e.g.:

```bash
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* **metadata**: specify SKIP to not push any new metadata (implicit or explicit)
* **_any other key_**: specify any other metadata key to store in the package

See below for more details.
See below for more details.
When running from the git repository,
you can use the Makefile to test the various options,
as long as you set a WRITE_BUCKET:
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make check
```

### Verifying NextFlow
### Verifying Nextflow

If this is your first time using NextFlow, you may also need to install a recent
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.
Nextflow itself will take care of all the other dependencies.

You can verify and compile NextFlow with:
You can verify and compile Nextflow with:

```bash
make nextflow
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