nextflow-dsl2

A Nextflow workflow to generate lift over files for any pair of genomes

A simple DSL2 workflow: tutorial

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

A repository for hosting Nextflow DSL2 module files containing tool-specific process definitions and their associated documentation for MSKCC

Automatized Polygenic Score Prediction

Nextflow workflow syntax highlighting and snippets for Sublime Text 4

Nextflow DSL2 tRNA and ncRNA fragment identification pipeline for small RNA-seq data

A Nextflow pipeline for integrated small RNA-seq and mRNA-seq analysis to uncover exercise-associated miRNA–mRNA regulatory networks.

This is a personal project focused on creating uniformal pipeline for processing RNA-seq data with the end goal to create a .Rdata object which can be imported into R/Shiny app for downstream analysis and hypothesis testing.

Nextflow DSL2 long-read RNA-seq pipeline: MisER splice correction → IsoQuant → oarfish → swish/fishpond differential expression (DTE/DTU/DGE)

Containerized Nextflow DSL2 workflow for viral intra-host variant calling (iSNV), quasispecies haplotype reconstruction, and evolutionary selection analysis.

Working through NextFlow tutorials. See https://github.com/nextflow-io/training

nextflow pipeline for BGC-QUAST tool

A modular Nextflow DSL2 pipeline implementing the GATK Best Practices for germline variant discovery from FASTQ preprocessing to functional variant annotation using Ensembl VEP.

Reproducible Nextflow DSL2 FASTQ QC pipeline with a hard validation gate - 42 unit tests, CI that verifies the gate fires

A small pipeline to generate genome statistics

Nextflow resequencing pipeline with bwa-mem and freebayes

Identifying allele-specific isoform expression with allspice🧂

Production Nextflow DSL2 germline variant calling pipeline with biomarker reproducibility analysis and AWS execution

A modular Nextflow DSL2 pipeline for reproducible plant de novo genome and transcriptome assembly, quality control, validation, and functional analysis.