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

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

A DSL for data-driven computational pipelines

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

Test data to be used for automated testing with the nf-core pipelines

Config files used to define parameters specific to compute environments at different Institutions

Code and files for the main nf-core website.

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

A single-cell RNAseq pipeline for 10X genomics data

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

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

A small-RNA sequencing analysis pipeline

Nextflow training material

ATAC-seq peak-calling and QC analysis pipeline

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Classic hello world script in Nextflow language

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

Assembly and binning of metagenomes

A proof of concept of RNAseq pipeline

RNA-seq analysis pipeline for detection of gene-fusions