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aspirational README
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drernie committed Aug 20, 2024
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Expand Up @@ -6,6 +6,8 @@ Nextflow plugin for reading and writing Quilt packages as a FileSystem
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.

In v0.8.0, the plugin can even be used with "native" URIs, and it will automatically register a Quilt package at the root of the bucket.

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

## I. Using the nf-quilt plugin in Production
Expand Down Expand Up @@ -35,6 +37,8 @@ You can alternatively specify the plugin as part of the command-line, .e.g.:
nextflow run ./main.nf -profile standard -plugins nf-quilt --outdir 'quilt+s3://bucket#package=prefix/suffix'
```

## II. Working With Quilt+ URIs (optional for output)

1. Obtain a Quilt+ URI for each package

Each Quilt+ package URI you read or write from has the form:
Expand Down Expand Up @@ -82,7 +86,7 @@ nextflow run main.nf -plugins [email protected]

For Tower, you can use the "Pre-run script" to set the environment variables.

## II. Advanced URI Options
## III. Advanced URI Options

There are a number of additional parameters you can add to Quilt+ URIs,
in order to customize the behavior of the plugin:
Expand Down Expand Up @@ -148,7 +152,7 @@ To quickly run `nf-quilt` from this GitHub repository:
```bash
git clone https://github.com/quiltdata/nf-quilt.git
cd nf-quilt
make test-all # runs unit tests and installs depdencies
make test-all # runs unit tests and installs dependencies
export WRITE_BUCKET=bucket-with-write-access
make pkg-test # create "test/hurdat" package on s3://$WRITE_BUCKET
./launch.sh run nf-core/sarek -profile test,docker -plugins nf-quilt \
Expand Down Expand Up @@ -195,9 +199,9 @@ type:
./launch.sh run ./main.nf -profile standard -plugins $(PROJECT) --pub "quilt+s3://bucket#package=test/hurdat"
```

Replace "bucket" with an S3 bucket those credentials can write to.
Replace "bucket" with an S3 bucket that those credentials can write to.

### Running a Pipeine Locally
### Running a Pipeline Locally

From inside the `nf-quilt` directory, call `./launch.sh` with a path to your pipeline.

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