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Nextflow Pipelines

Nextflow pipelines hosted in Git repositories. Each published release records the Git revision it runs and the launch configuration it ships with.

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32 pipeline(s) matching "st".

Pipeline Keywords Description
nf-core/proteinfold
2.0.0
 alphafold2 colabfold esmfold protein-fold-prediction +3 Protein 3D structure prediction pipeline
nf-core/raredisease
3.1.2
 diagnostics rare-disease snv structural-variants +4 Call and score variants from WGS/WES of rare disease patients.
nf-core/rarevariantburden
0.0.0-3ba9926
 burden-test cocorv public-data-as-controlset rarevariant Pipeline for performing consistent summary count based rare variant burden test, which is useful when we only have sequenced cases data. For example, we can compare the cases against public summary count data, such as gnomAD.
nf-core/rnastructurome
1.0.0
 dms map rna-structure rnacentral +3 a bioinformatics pipeline for analysing chemical high-throughput RNA structure-probing data
nf-core/scdownstream
0.0.0-3c2644c
 clustering dimensionality-reduction integration quality-control +2 A single cell transcriptomics pipeline for QC, integration and making the data presentable
nf-core/scrnaseq
4.2.0
 10x-genomics 10xgenomics alevin bustools +5 Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
nf-core/spatialvi
0.0.0-17d6cb0
 10x-genomics 10xgenomics image-processing microscopy +7 Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
nf-core/ssds
0.0.0-0cc3ee6
 chip-ssds dmc1-ssds dsbs ori-ssds +4 Single-stranded DNA Sequencing (SSDS) nf-core pipeline
nf-core/stableexpression
1.1.0
 expression housekeeping-genes qpcr-analysis This pipeline is designed to identify the most stable genes in one or more expression datasets (RNA-seq / Microarray). The ideal use case is for determining the most suitable RT-qPCR reference genes for a given species.
nf-core/troughgraph
0.0.0-c3e250e
 permafrost A quantitative assessment of the underlying permafrost landscapes and, per extension, of the level of permafrost thaw in the region
nf-core/variantbenchmarking
1.5.0
 benchmark small-variants structural-variants variant-calling Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research
nf-core/viralmetagenome
1.2.0
 epidemiology fastq ngs viral-metagenomics +2 A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
Nextflow Registry v0.28.0_c73a300 - 12 Oct 2026 09:32:30 (UTC)