55 projects
snakemake-report-plugin-nanopub
Reporter plugin for Snakemake using nanopub-py to create workflow metadata nanopubs
snakefmt
The uncompromising Snakemake code formatter
snakemake-storage-plugin-xrootd
A Snakemake storage plugin for XRootD storage
snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster.
snakemake
Workflow management system to create reproducible and scalable data analyses
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)
ddargparse
Dataclass driven argparse handling
snakemake-interface-logger-plugins
Logger plugin interface for snakemake
snakemake-scheduler-plugin-milp
A Snakemake scheduler plugin using Mixed-Integer Linear Programming (MILP).
snakemake-scheduler-plugin-greedy
A greedy Snakemake scheduler plugin.
kisiac
None
snakemake-interface-storage-plugins
This package provides a stable interface for interactions between Snakemake and its storage plugins.
snakemake-scheduler-plugin-firstfit
A Snakemake scheduler plugin that selects the first jobs that fit available resources.
snakemake-storage-plugin-http
Snakemake storage plugin for downloading input files from HTTP(s).
snakemake-software-deployment-plugin-conda
Software deployment plugin for Snakemake using rattler to deploy conda packages.
snakemake-interface-software-deployment-plugins
This package provides a stable interface for interactions between Snakemake and its software deployment plugins.
snakemake-software-deployment-plugin-container
None
vembrane
Filter VCF/BCF files with Python expressions.
snakemake-interface-report-plugins
The interface for Snakemake report plugins.
snakemake-interface-common
Common functions and classes for Snakemake and its plugins
snakemake-interface-executor-plugins
This package provides a stable interface for interactions between Snakemake and its executor plugins.
snakemake-software-deployment-plugin-envmodules
Software deployment plugin for Snakemake using environment modules.
spectrseqtools
SpectrSeqTools is a fully automatic analysis platform for sequencing small RNA molecules including 144 known post translational modifications measured via LC-MS/MS data.
snakedeploy
Deployment and maintenance related toolbox for Snakemake
snakemake-executor-plugin-googlebatch
None
yte
A YAML template engine with Python expressions
snakemake-storage-plugin-fs
A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync
snakemake-interface-scheduler-plugins
Scheduler plugin interface for snakemake
snakemake-wrapper-utils
A collection of utils for Snakemake wrappers.
snakemake-storage-plugin-s3
A Snakemake storage plugin for S3 API storage (AWS S3, MinIO, etc.)
snakemake-executor-plugin-kubernetes
A snakemake executor plugin for submission of jobs to Kubernetes
snakemake-executor-plugin-cluster-sync
A Snakemake executor plugin for cluster jobs that are executed synchronously.
poetry-snakemake-plugin
A plugin for poetry that adds Snakemake-specific functionality.
snakemake-storage-plugin-irods
A Snakemake plugin for handling input and output on iRODS
snakemake-storage-plugin-sftp
A Snakemake storage plugin that handles files on an SFTP server.
snakemake-storage-plugin-ftp
A Snakemake plugin for handling input and output via FTP
snakemake-storage-plugin-zenodo
A Snakemake storage plugin for reading from and writing to zenodo.org
snakemake-storage-plugin-webdav
None
snakemake-storage-plugin-gcs
A Snakemake storage plugin for Google Cloud Storage
snakemake-storage-plugin-azure
A Snakemake storage plugin to read and write from Azure Blob Storage
snakemake-executor-plugin-aws-batch
Snakemake executor plugin for AWS Batch
snakemake-executor-plugin-drmaa
A snakemake executor plugin for submission of jobs via DRMAA.
snakemake-executor-plugin-azure-batch
A Snakemake executor plugin for submitting jobs to Microsoft Azure Batch.
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-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-cluster-generic
ytml
A YAML based HTML templating engine
snakemake-executor-plugin-kueue
snakemake-object
Language agnostic encoding of Snakemake job information as 'Snakemake objects' into Snakemake script preambles.
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
