The drake R package
The drake R package: a pipeline toolkit for reproducibility and high-performance computing - Published in JOSS (2018)
The targets R package
The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing - Published in JOSS (2021)
VeridicalFlow
VeridicalFlow: a Python package for building trustworthy data science pipelines with PCS - Published in JOSS (2022)
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity
Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity - Published in JOSS (2017)
cwl_runner
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
Baargin
Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)
dockstore
An app store for scientific workflows, tools, notebooks, and services
scrnaseq
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
weaver
Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package
airrflow
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
funcscan
(Meta-)genome screening for functional and natural product gene sequences
epitopeprediction
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
pipelines-nextflow
A set of workflows written in Nextflow for Genome Annotation.
crisprseq
A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).
bamtofastq
Converts bam or cram files to fastq format and does quality control.
academic-observatory-workflows
Telescopes, Workflows and Data Services for the Academic Observatory
mcmicro
An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
circdna
Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
aiida-kkr
AiiDA plugin of the high-performance density functional theory code JuKKR (www.judft.de) for high-throughput electronic structure calculations.
genomeassembler
Assembly and scaffolding of haploid / unphased genomes from long ONT or PacBio HiFi reads
Cylc
Cylc: A Workflow Engine for Cycling Systems - Published in JOSS (2018)
dea_limma
A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.
oaebu-workflows
Telescopes, Workflows and Data Services for the 'Book Analytics Dashboard Project (2022-2025)', building upon the project 'Developing a Pilot Data Trust for Open Access eBook Usage (2020-2022)'
pyiron_base
Core components of the pyiron integrated development environment (IDE) for computational materials science
spilterlize_integrate
A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.
mixscape_seurat
A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.
teeplot
organize data visualization output, automatically picking meaningful names based on semantic plotting variables
dea_seurat
A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
https://github.com/agnostiqhq/covalent
Pythonic tool for orchestrating machine-learning/high performance/quantum-computing workflows in heterogeneous compute environments.
rangeland
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
pymialsrtk
The Medical Image Analysis Laboratory Super-Resolution ToolKit (MIALSRTK) consists of a set of C++ and Python processing and workflow tools necessary to perform motion-robust super-resolution fetal MRI reconstruction in the BIDS Apps framework.
https://github.com/common-workflow-language/cwlviewer
A web application to view and share Common Workflow Language workflows
polyaxon
MLOps Tools For Managing & Orchestrating The Machine Learning LifeCycle
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
differentialabundance
Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
fastquorum
Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
Spine-Toolbox
Spine Toolbox is an open source Python package to manage data, scenarios and workflows for modelling and simulation. You can have your local workflow, but work as a team through version control and SQL databases.
https://github.com/flyteorg/flyte
Scalable and flexible workflow orchestration platform that seamlessly unifies data, ML and analytics stacks.
circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
metatdenovo
Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.
test-datasets
Test data to be used for automated testing with the nf-core pipelines
molkart
A pipeline for processing Molecular Cartography data from Resolve Bioscience (combinatorial FISH)
https://github.com/aiidateam/aiida-core
The official repository for the AiiDA code