A template for standard compliant snakemake-workflows
☆133Mar 27, 2026Updated last month
Alternatives and similar repositories for snakemake-workflow-template
Users that are interested in snakemake-workflow-template are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A workflow for creating small NGS test data sets, useful for continuous integration.☆24Aug 15, 2024Updated last year
- RNA-seq workflow using STAR and DESeq2☆362Dec 18, 2025Updated 5 months ago
- Cookiecutter for snakemake slurm profile☆135Apr 25, 2024Updated 2 years ago
- A statically generated catalog of available Snakemake workflows☆36May 18, 2026Updated last week
- A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.☆69Mar 19, 2026Updated 2 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- This is the development home of the Snakemake wrapper repository, see☆243Updated this week
- deploy a snakemake pipeline directly from version control (under development)☆25Mar 12, 2026Updated 2 months ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13May 7, 2026Updated 2 weeks ago
- A cookiecutter template for Snakemake workflows☆59Feb 2, 2022Updated 4 years ago
- A Github action for running a Snakemake workflow☆62Apr 24, 2026Updated last month
- This Snakemake pipeline implements the GATK best-practices workflow☆265Jun 8, 2023Updated 2 years ago
- Documentation of the Snakemake-Workflows project☆158Feb 2, 2022Updated 4 years ago
- The uncompromising Snakemake code formatter☆190Updated this week
- A *fast* tool for BAM/CRAM quality evaluation, intended for long reads☆185May 4, 2026Updated 3 weeks ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- This is the development home of the workflow management system Snakemake. For general information, see☆2,781May 14, 2026Updated last week
- Snakemake tutorial materials☆19Mar 9, 2020Updated 6 years ago
- Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)☆15Updated this week
- Snakemake workflow management system and CLI generation tool☆67Oct 22, 2025Updated 7 months ago
- ⛰ covtobed | Convert the coverage track from a BAM file into a BED file☆44Nov 6, 2025Updated 6 months ago
- Language support and snippets for Snakemake workflows (Snakefile, *.smk) for Visual Studio Code and Apache Theia.☆23Updated this week
- Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu☆21Updated this week
- A Snakemake executor plugin for submitting jobs to a SLURM cluster☆52Apr 17, 2026Updated last month
- A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, …☆90May 17, 2026Updated last week
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- A place to put docker build files☆14Oct 3, 2023Updated 2 years ago
- Genome scale metabolic models in SBML format☆11Nov 16, 2021Updated 4 years ago
- Cookiecutter profile for making a NextFlow-based bioinformatics tool☆17Jul 8, 2024Updated last year
- A TUI for monitoring Snakemake workflows in real-time.☆61Mar 13, 2026Updated 2 months ago
- Best practices and workflow for genome annotation☆78Apr 14, 2025Updated last year
- Code associated with MIX-seq manuscript☆15Aug 26, 2020Updated 5 years ago
- A program for the analysis of single cell nanopore long read data☆21Jul 1, 2025Updated 10 months ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10May 1, 2026Updated 3 weeks ago
- Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.☆22Feb 9, 2026Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Documentation of the Snakemake-Profiles project.☆55Mar 15, 2022Updated 4 years ago
- Snakemake profile for running jobs on an LSF cluster☆38Jul 29, 2024Updated last year
- Cookiecutter profile for making a Snakemake-based bioinformatics tool, but without the fluff☆52Oct 17, 2023Updated 2 years ago
- Arima Capture HiC pipeline (Arima-CHiC)☆14May 16, 2024Updated 2 years ago
- ☆17May 4, 2026Updated 3 weeks ago
- Listing of GPU based bioinformatics software & sites & publications☆12Jan 16, 2022Updated 4 years ago
- A DRAFT, early stage book on snakemake.☆22Nov 1, 2023Updated 2 years ago