nf-core / modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
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Repository to host tool-specific module files for the Nextflow DSL2 community!
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Nextflow training material
Assembly and binning of metagenomes
Nanopore demultiplexing, QC and alignment pipeline
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
Amplicon sequencing analysis workflow using DADA2 and QIIME2
Pipeline to fetch metadata and raw FastQ files from public databases
B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework
Assembly and intrahost/low-frequency variant calling for viral samples
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
RNA-seq analysis pipeline for detection of gene-fusions
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Config files used to define parameters specific to compute environments at different Institutions
A comprehensive cancer DNA/RNA analysis and reporting pipeline
gatk4 RNA variant calling pipeline