40 projects
snakedeploy
Deploy a snakemake pipeline from GitHub
snakemake
Workflow management system to create reproducible and scalable data analyses
snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster.
snakemake-storage-plugin-fs
A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync
snakemake-storage-plugin-s3
A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
snakemake-interface-storage-plugins
This package provides a stable interface for interactions between Snakemake and its storage plugins.
snakefmt
The uncompromising Snakemake code formatter
snakemake-interface-executor-plugins
This package provides a stable interface for interactions between Snakemake and its executor plugins.
snakemake-executor-plugin-slurm-jobstep
A Snakemake executor plugin for running srun jobs inside of SLURM jobs (meant for internal use by snakemake-executor-plugin-slurm)
snakemake-interface-common
Common functions and classes for Snakemake and its plugins
snakemake-executor-plugin-googlebatch
None
snakemake-storage-plugin-xrootd
A Snakemake storage plugin for xrootd storage
snakemake-executor-plugin-drmaa
A snakemake executor plugin for submission of jobs via DRMAA.
snakemake-executor-plugin-cluster-sync
A Snakemake executor plugin for cluster jobs that are executed synchronously.
snakemake-executor-plugin-tes
A Snakemake executor plugin for submitting jobs via GA4GH TES.
snakemake-executor-plugin-flux
A snakemake executor plugin for the Flux scheduler
snakemake-executor-plugin-kubernetes
A snakemake executor plugin for submission of jobs to Kubernetes
snakemake-executor-plugin-cluster-generic
snakemake-storage-plugin-gcs
A Snakemake storage plugin for Google Cloud Storage
snakemake-storage-plugin-irods
A Snakemake plugin for handling input and output on iRODS
snakemake-storage-plugin-azure
A Snakemake storage plugin to read and write from Azure Blob Storage
poetry-snakemake-plugin
A plugin for poetry that adds Snakemake-specific functionality.
snakemake-interface-report-plugins
The interface for Snakemake report plugins.
ytml
A YAML based HTML templating engine
snakemake-storage-plugin-ftp
A Snakemake plugin for handling input and output via FTP
snakemake-executor-plugin-kueue
snakemake-executor-plugin-azure-batch
A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.
snakemake-storage-plugin-webdav
yte
A YAML template engine with Python expressions
snakemake-storage-plugin-http
Snakemake storage plugin for donwloading input files from HTTP(s).
snakemake-storage-plugin-zenodo
A Snakemake storage plugin for reading from and writing to zenodo.org
snakemake-storage-plugin-sftp
A Snakemake storage plugin that handles files on an SFTP server.
conda-inject
Helper functions for injecting a conda environment into the current python environment (by modifying sys.path, without actually changing the current python environment).
snakemake-object
Language agnostic encoding of Snakemake job information as 'Snakemake objects' into Snakemake script preambles.
snakemake-wrapper-utils
A collection of utils for Snakemake wrappers.
calfreeslots
Command line utility to print free calendar slots in the coming days.
vispr
Interactive HTML5 visualization for CRISPR/Cas9 knockout screen experiments.
peanut
A massively parallel GPU read mapper using OpenCL.
alpaca-variant-caller
An algebraic parallel SNV caller using OpenCL
trminer
mine scientific publications for interesting sentences using patterns
