Nextflow Plugin
Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. The software is used by scientists and engineers to write, deploy and share data-intensive, highly scalable, workflows on any infrastructure.
nf-quilt
is a Nextflow plugin developed by Quilt Data that enables you read and write directly to Quilt data packages instead of just S3 locations.
Quick Start
All you need to do is add the nf-quilt
plugin to a Nextflow pipeline that writes to Amazon S3. The plugin will automatically create a Quilt package with metadata from each run. You can do this in one of three ways.
Add it to the command-line:
Include it in the nextflow config file (e.g.,
main.nf
):Specify it in the Advanced Options for a Seqera Platform job:
Using Earlier Versions
To use older versions of nf-quilt
, you can specify the version number of the plugin using the '@' sign:
Using Prerelease Versions
To use unreleased versions of the nf-quilt
plugin, you must also set the location using environment variable. For example, to use version 0.8.6, set NXF_PLUGINS_TEST_REPOSITORY
from the command-line or the "Pre-run script" of the Seqera Platform:
Output and Input URIs
The canonical reference to a package is defined by a quilt+
URI. For example, the s3://quilt-example-bucket/test/nf_quilt_rnaseq
S3 URI will create a package with the Quilt URI:
You can then use that URI as input to future jobs, and similar URIs for the output, e.g.,
Additional Features
The nf-quilt
plugin supports a wide range of additional options for configuring input, output, and metadata. For more details, or to participate in the development, please visit the quiltdata/nf-quilt GitHub repository.
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