nextflow

A DSL for data-driven computational pipelines

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

A curated list of nextflow based pipelines

A flexible pipeline for complete analysis of bacterial genomes

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Repository to host tool-specific module files for the Nextflow DSL2 community!

A curated collection of Nextflow implementation patterns

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

GCP for Bioinformatics Researchers

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

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Assembly and binning of metagenomes

Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line

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

ATAC-seq peak-calling and QC analysis pipeline

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Nanopore demultiplexing, QC and alignment pipeline

Pipeline to fetch metadata and raw FastQ files from public databases

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

A fully reproducible and state-of-the-art ancient DNA analysis pipeline