Nextflow Plugin
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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 developed by Quilt
Data that enables you read and write directly to instead of just S3 locations.
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:
To use older versions of nf-quilt, you can specify the version number of the
plugin using the '@' sign:
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, setNXF_PLUGINS_TEST_REPOSITORY from the command-line or the "Pre-run script" of
the Seqera Platform:
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.,
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 GitHub repository.
