nvnieuwk
Bioinformatician at CMGG | nf-core core member | nf-core maintainer | Nextflow ambassador
Center for Medical Genetics GhentGhent, Belgium
Pinned Repositories
nf-schema
Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines
germline
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
structural
A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
bedgovcf
A simple tool to convert BED files to VCF files
cookiecutter-nftest-plugin
A cookiecutter template for an nf-test plugin
multi-package-containers
Testing building mulled containers for multi-requirement tools.
nf-samplesheet-conversion
A script to validate a samplesheet and convert it to a Nextflow channel.
nf-test-snippets
A collection of snippets to use for nf-test assertions
nft-bam
An nf-test plugin for reading the contents of SAM/BAM/CRAM files in assertions
svync
A tool to standardize VCF files from structural variant callers
nvnieuwk's Repositories
nvnieuwk/nft-bam
An nf-test plugin for reading the contents of SAM/BAM/CRAM files in assertions
nvnieuwk/bedgovcf
A simple tool to convert BED files to VCF files
nvnieuwk/nf-test-snippets
A collection of snippets to use for nf-test assertions
nvnieuwk/cookiecutter-nftest-plugin
A cookiecutter template for an nf-test plugin
nvnieuwk/multi-package-containers
Testing building mulled containers for multi-requirement tools.
nvnieuwk/bioconda-recipes
Conda recipes for the bioconda channel.
nvnieuwk/configs
Config files used to define parameters specific to compute environments at different Institutions
nvnieuwk/svync
A tool to standardize VCF files from structural variant callers
nvnieuwk/bytesize-nft-bam
Repository that contains all the content used for the nft-bam bytesize of July 30th 2024
nvnieuwk/nextflow
A DSL for data-driven computational pipelines
nvnieuwk/nextflow-demo
A demonstration on how to easily run a Nextflow pipeline and how easy it is to create one
nvnieuwk/nextflow-watchpath-samplesheet
A POC implementation of the `.watchPath` Nextflow channel factory in combination with a samplesheet
nvnieuwk/nextflow_schema
A repository to host meta JSON schemas for Nextflow
nvnieuwk/nf-cmgg-structural
Nextflow workflow for calling structural variants
nvnieuwk/nf-co.re
Code and files for the main nf-core website.
nvnieuwk/nf-core-modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
nvnieuwk/nf-ga4gh
GA4GH plugin for Nextflow
nvnieuwk/nf-test
Simple test framework for Nextflow pipelines
nvnieuwk/nf-test-plugins
Repository for nf-test plugins
nvnieuwk/nf-validation
Params validation plugin for Nextflow pipelines
nvnieuwk/nf-validation-demo
A repository for demonstrating nf-validation
nvnieuwk/nft-utils
nf-test utility functions
nvnieuwk/pipeception
A small POC pipeline testing out how to run pipelines inside of another pipeline
nvnieuwk/plugins
Nextflow plugins index repository
nvnieuwk/python-scripts
A repository containing a collection of some useful small Python scripts I wrote
nvnieuwk/testpipeline
A small example pipeline used to test new nf-core infrastructure and common code.
nvnieuwk/tools
Python package with helper tools for the nf-core community.
nvnieuwk/variantbenchmarking
A nextflow variant benchmarking pipeline - premature
nvnieuwk/vibbits-nextflow-workshop
Nextflow workshop materials March 2023
nvnieuwk/website
Nextflow public web site