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nf-core: Community-Curated Nextflow Pipelines

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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