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 curated collection of Nextflow implementation patterns

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

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

A flexible pipeline for complete analysis of bacterial genomes

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

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

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

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

ATAC-seq peak-calling, QC and differential analysis pipeline

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Nextflow Tower system

Assembly and binning of metagenomes

GATK RNA-Seq Variant Calling in Nextflow

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Our VM/Docker sharing infrastructure and management component

Nanopore demultiplexing, QC and alignment pipeline

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