Nextflow Python Packages

nf-core

Python package with helper tools for the nf-core community.

pytest-workflow

Configure workflow/pipeline tests using yaml files.

contig

An agentic bioinformatics analyst: it runs the analysis on your own compute, self-heals failures, verifies the output, and returns a reproducible result.

nextflowpy

Python wrapper around Nextflow.

turbo-picard

Picard-compatible Rust tools for faster SAM/BAM/CRAM, VCF, duplicate-marking and sequencing-QC workflows.

nf-metro

Metro-map-style SVG diagrams from Mermaid graph definitions, designed for visualizing bioinformatics pipeline workflows

clew-lineage

Lineage-based impact analysis and remediation for workflow runs. What a bad input or an incident report reached, what to re-run, delete or disclose, sealed as evidence an auditor verifies offline. Incident triage, MCP tools for agents, agent-written providers. Reads Nextflow, Snakemake, Cromwell, Horus, DNAnexus and Latch.

quantms-utils

A python library with scripts and helpers classes for quantms workflow

monsda

MONSDA, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

workflow-clinic

GA4GH Workflow Clinic

micone

The Microbial Co-occurrence Network Explorer

cloudfit-core

Cloud-agnostic machine type scoring engine for bioinformatics workloads

flowcraft

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

virpipe

Composable pipeline framework for virus detection in high-throughput sequencing data

assemblerflow

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

pybrave

BRAVE (Bioinformatics Reactive Analysis and Visualization Engine) bridges the gap between engineering and scientific research

covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

cbicall

CBIcall is a configuration-driven framework for reproducible variant calling in large sequencing cohorts, enabling standardized pipelines from FASTQ to analysis-ready VCFs across heterogeneous computing environments.

nf-runinsights-dashboard

Nextflow plugin for cross-run benchmarking. Records per-process metrics for every run into a local or shared history store, compares runs against their own history, and flags regressions with likely causes, over-provisioned resources, and retries. Includes a zero-dependency dashboard, an MCP server for AI assistants, and opt-in AI narration.

nflaunch

nflaunch is a command-line tool to simplify launching Nextflow pipelines on cloud batch services (GCP Batch)

py-nf

Python library to execute batches of jobs using nextflow.

nf-python-plugin

Nextflow plugin enabling seamless integration between Nextflow and Python 🧪

metasheet-guard

Experimental-design-aware QC, repair, and workflow export for sequencing analysis sample sheets.

sceptr-profiling

Continuous enrichment profiling for transcriptomes. Characterise how functional programmes are distributed across the expression gradient, with built-in significance testing for single samples. Great for non-model organisms, clinical isolates, and unreplicated datasets.