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

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

A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

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

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

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

A flexible pipeline for complete analysis of bacterial genomes

Our VM/Docker sharing infrastructure and management component

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

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

Nextflow Tower system

GATK RNA-Seq Variant Calling in Nextflow

A graphical user interface for distributed data processing of high throughput genomics

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

16S rRNA amplicon sequencing analysis workflow using QIIME2

Nextflow pipeline for analysis of direct RNA Nanopore reads

Example Nextflow pipelines and programming techniques

RNA-seq analysis pipeline for detection gene-fusions

WtP: Phage identification via nextflow and docker or singularity

Assembly and binning of metagenomes

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

Assembly and intrahost/low-frequency variant calling for viral samples

Multi-sample somatic variant caller

A modular Hi-C mapping pipeline

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