pipemake
pipemake is a lightweight, flexible, and easy-to-use tool for creating and managing Snakemake pipelines. It makes Snakemake’s reproducibility safeguards automatic, reusable, and accessible to researchers who would otherwise struggle to implement them. It was designed with four primary goals:
Offer a collection of curated, customizable genomic analysis pipelines for researchers seeking to rapidly integrate Snakemake-based workflows into their research.
Build safeguards into every pipeline as enforced defaults, including validated command-line arguments, mandatory containerization, and standardized record-keeping in a workflow directory.
Optimize computational efficiency and reproducibility by fully operating in the Snakemake ecosystem. pipemake generates standard Snakemake files, so a workflow can be run with Snakemake alone.
Streamline development and sharing by creating a flexible platform with swappable pipelines that easily reuse previously written Snakemake code, allowing a group to maintain and share a single collection of pipelines.
pipemake is most useful for analyses that need to be repeated, shared, or reproduced by someone other than the original designer, such as in research groups whose members have different levels of computational expertise. It is not intended to replace community-curated pipelines, such as those from nf-core, where one already exists for the analysis.
Getting pipemake
mamba
mamba create -c conda-forge -c bioconda kocherlab::pipemakeFor more information, see the installation instructions.
Issues
Check the docs.
Search the issues on GitHub or open a new one.
Contributors
Andrew Webb, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA, Howard Hughes Medical Institute, Chevy Chase, MD, USA
Scott Wolf, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
Ian M Traniello, Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
Sarah Kocher, Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA, Howard Hughes Medical Institute, Chevy Chase, MD, USA
License
Pipemake is licensed under the MIT license. See the LICENSE file for details.
1 maintainer
Metadata
1 maintainer
Release files for pipemake 1.5.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pipemake-1.5.3.tar.gz | 33.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pipemake-1.5.3-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 63.5 kB
Release files / pipemake-1.5.3.tar.gz
| Download URL | pipemake-1.5.3.tar.gz |
|---|---|
| Size | 33.9 kB |
| Tags | Source |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.9.25
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Release files / pipemake-1.5.3-py3-none-any.whl
| Download URL | pipemake-1.5.3-py3-none-any.whl |
|---|---|
| Size | 29.6 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.9.25
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