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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Nextflow 157 149 Updated Feb 4, 2025

AlphaFold 3 inference pipeline.

Python 6,070 746 Updated Feb 14, 2025

Stochastic Testing and Input Manipulation for Unbiased Learning Systems

Nextflow 25 12 Updated Feb 19, 2025

A collection of snippets to use for nf-test assertions

Nextflow 2 Updated Mar 29, 2024

Aggregate results from bioinformatics analyses across many samples into a single report.

JavaScript 1,267 612 Updated Feb 9, 2025

nf-core pipeline for comparative analysis of ortholog predictions

Nextflow 10 5 Updated Feb 5, 2025

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

C 104 39 Updated Feb 17, 2025

nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks

Nextflow 8 3 Updated Feb 6, 2025

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 t…

Nextflow 38 28 Updated Feb 19, 2025

A playground to explore how to implement things in Nextflow and nf-core

Shell 6 4 Updated Feb 19, 2025

Simple test framework for Nextflow pipelines

Java 151 26 Updated Dec 28, 2024

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

Nextflow 27 12 Updated Feb 19, 2025

MARS-seq v2 pre-processing pipeline with velocity

Nextflow 6 4 Updated Jan 27, 2025

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Python 375 44 Updated Dec 1, 2023

Params validation plugin for Nextflow pipelines

Groovy 48 18 Updated Aug 7, 2024

Instructions and scripts for custom GitHub Actions runners

Shell 2 4 Updated Jan 29, 2025

Protein 3D structure prediction pipeline

Nextflow 70 49 Updated Feb 19, 2025

ATAC-seq peak-calling and QC analysis pipeline

Nextflow 197 125 Updated Feb 12, 2025

GitHub Action to launch a workflow using Nextflow Tower.

Shell 12 6 Updated Mar 28, 2023

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Nextflow 984 721 Updated Feb 11, 2025

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

Nextflow 36 18 Updated Jan 27, 2025

Code and files for the main nf-core website.

MDX 69 220 Updated Feb 20, 2025

A small-RNA sequencing analysis pipeline

Nextflow 79 126 Updated Jan 27, 2025

ChIP-seq peak-calling, QC and differential analysis pipeline.

Nextflow 206 149 Updated Jan 27, 2025

Agent app that allows connecting remote batch schedulers to Tower Cloud

Java 8 5 Updated Dec 16, 2024

A collection of unexpected challenges and learnings with nextflow and nf-core.

Shell 34 9 Updated Oct 17, 2023

Making Protein folding accessible to all!

Jupyter Notebook 2,100 518 Updated Jan 16, 2025

A RNA-seq differential expression analysis pipeline downstream of nf-core/rnaseq.

R 6 5 Updated Jun 30, 2022

Testing building mulled containers for multi-requirement tools.

70 223 Updated Feb 11, 2025

DSL2 NextFlow wrapped CAGE-Seq analysis pipeline from demultiplexing to base pair resolution read counting (i.e. compatible import to CAGEfightR)

Makefile 3 2 Updated Aug 29, 2022
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