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

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

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

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

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

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, QC and differential analysis pipeline

Nextflow Tower system

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

Assembly and binning of metagenomes

Amplicon sequencing analysis workflow using DADA2 and QIIME2

GATK RNA-Seq Variant Calling in Nextflow

Nanopore demultiplexing, QC and alignment pipeline

Our VM/Docker sharing infrastructure and management component

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