cookiecutter-snakemake-workflow
atlas
| cookiecutter-snakemake-workflow | atlas | |
|---|---|---|
| 1 | 2 | |
| 55 | 349 | |
| - | 2.0% | |
| 1.8 | 8.9 | |
| over 2 years ago | 22 days ago | |
| Python | Python | |
| MIT License | BSD 3-clause "New" or "Revised" License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
cookiecutter-snakemake-workflow
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Development notes in Snakemake workflows
I currently use cookiecutter to start new Snakemake repositories (projects) because it's really comfortable and guarantees that I follow an organized and recommended directory structure. However, I have a tendency to make notes during development. Maybe I made some decision based on something I learned in biostars or reddit and I want to remember that, or I start by outlining my workflow steps in written form. So far I've used both the README file and the Snakemake file (comments) to do that, but I'm wondering if anyone has a suggestion for how to fit development notes within a Snakemake project.
atlas
- Resources to learn genetic data manipulation basics?
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Is it possible to calculate relative abundance of microorganisms in a community through shotgun-metagenomics?
You might want to check Atlas, an assembly/binning based pipeline for metagenomics data Publication Github
What are some alternatives?
cookiecutter-data-science - A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
pypsa-eur - PyPSA-Eur: A Sector-Coupled Open Optimisation Model of the European Energy System
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
FastAPI-template - Feature rich robust FastAPI template.
zarp - The Zavolab Automated RNA-seq Pipeline
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
chipseq-smk-pipeline - ChIP-Seq processing pipeline on snakemake
eggnog-mapper - Fast genome-wide functional annotation through orthology assignment
bioinformatics - :microscope: Path to a free self-taught education in Bioinformatics!