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Overview

Nf-core is the largest community-driven platform for curated bioinformatics workflow development. The RIVER platform is designed with nf-core as its primary focus, executing Nextflow pipelines directly on HPC infrastructure with native S3 integration, without requiring middleware layers. The platform is engineered to support all existing nf-core pipelines.

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Running Nextflow pipelines with nf-core can present unique challenges and considerations. Our team provides detailed blog posts demonstrating how to execute these pipelines with real datasets and optimize them as needed.

Tested Pipelines:

  1. sarek: Variant calling pipeline for germline and somatic variants from whole genome, exome, or targeted sequencing data. Supports tumor/normal analyses.
  2. rnaseq: RNA-seq processing pipeline that includes quality control, alignment or pseudo-alignment, quantification, and generation of gene expression matrices.
  3. ampliseq: Amplicon sequencing pipeline for microbial community profiling, such as 16S rRNA gene sequencing.
  4. quantms: Quantitative proteomics pipeline for label-free and isobaric labeling analyses using both DDA and DIA data.
  5. taxprofiler: Taxonomic profiling pipeline for shotgun metagenomics, supporting multiple tools and producing standardized outputs.
  6. methylseq: DNA methylation analysis pipeline using bisulfite-treated sequencing data. Supports multiple aligners and provides comprehensive QC.
  7. circrna: Pipeline for detecting and quantifying circular RNAs (circRNAs) from RNA-seq data, including miRNA target prediction.
  8. mag: Metagenomic pipeline for assembling, binning, and annotating metagenome-assembled genomes (MAGs) from short or long reads.
  9. atacseq: ATAC-seq pipeline to identify open chromatin regions, perform peak calling, and assess data quality with various QC metrics.
  10. rnafusion: Fusion detection pipeline using RNA-seq data, combining results from multiple fusion detection tools into reports and visualizations.