nf-core: Community-Curated Nextflow Pipelines
The nf-core project is a community-driven effort to create a curated collection of Nextflow pipelines for bioinformatics analysis. The pipelines are developed and maintained by bioinformaticians and computational biologists from around the world, and are designed to be portable, scalable, and reproducible.
The complete list of nf-core pipelines is available on the nf-core website. Cirro provides a subset of nf-core pipelines that are available for analysis on the platform. Please reach out if there is a pipeline that you would like to see added.
nf-core Pipelines Available on Cirro
Analysis | Workflow | Version |
---|---|---|
ATAC-seq | nf-core/atacseq | 2.0 |
Bisulfite DNA Methylation | nf-core/methylseq | 1.6.1 |
ChIP-seq | nf-core/chipseq | 2.0 |
CUT&RUN | nf-core/cutandrun | 2.0 |
De Novo Bacterial Genome Assembly | nf-core/bacass | 2.1.0 |
Differential Gene Expression | nf-core/differentialabundance | 1.5.0 |
Germline / Somatic DNA Variant Calling | nf-core/sarek | 3.4.2 |
Metagenome-Assembled Genome (MAG) | nf-core/mag | 3.0.0 |
Microbiome 16S | nf-core/ampliseq | 2.7.0 |
NanoString nCounter | nf-core/nanostring | 1.2.1 |
Quantitative Mass Spectrometry - DDA-LFQ | nf-core/quantms | 1.2.0 |
RNA Fusion | nf-core/rnafusion | 2.1.0 |
RNAseq Gene Expression | nf-core/rnaseq | 3.14.0 |