oamd-bio-test-data

This repository contains test data to be used for automated testing of Advance Molecular Detection Platform pipelines.

⚠️ Do not merge your test data to master! Each pipeline has a dedicated branch (and a special one for modules)

Introduction

ph-core's set up mirrors that of nf-core. ph-core is a collection of high quality Nextflow workflows, subworkflows, and modules related to genomic surveillance. This repository contains various files for CI and unit testing of ph-core pipelines and infrastructure.

The principle for ph-core test data is the same as nf-core test data in that the data should be as small as possible, as large as necessary. Please see the guidelines for nf-core test datasets for more detailed information.

Downloading test data

Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use.

bash git clone <url> --single-branch --branch <pipeline/modules/branch_name>

To subsequently clone other branches[^1]

bash git remote set-branches --add origin [remote-branch] git fetch

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

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Contributing Standard Notice

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Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.