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

A curated collection of Nextflow implementation patterns

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

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

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

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

Call and score variants from WGS/WES of rare disease patients.

A small-RNA sequencing analysis pipeline

Differential gene expression analysis and pathway analysis of RNAseq data

Please consider using/contributing to https://github.com/nf-core/sarek

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.