nextflow
There are 717 repositories under nextflow topic.
nextflow-io/nextflow
A DSL for data-driven computational pipelines
nf-core/rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
nextflow-io/awesome-nextflow
A curated list of nextflow based pipelines
bactopia/bactopia
A flexible pipeline for complete analysis of bacterial genomes
nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
nextflow-io/patterns
A curated collection of Nextflow implementation patterns
nf-core/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
assemblerflow/flowcraft
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:
lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
nf-core/tools
Python package with helper tools for the nf-core community.
nvuillam/npm-groovy-lint
Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line
nf-core/mag
Assembly and binning of metagenomes
nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
nf-core/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
nf-core/atacseq
ATAC-seq peak-calling and QC analysis pipeline
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
nf-core/nanoseq
Nanopore demultiplexing, QC and alignment pipeline
seqeralabs/nf-tower
Nextflow Tower system
nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
SciLifeLab/Sarek
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
CRG-CNAG/CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
askimed/nf-test
Simple test framework for Nextflow pipelines
nf-core/fetchngs
Pipeline to fetch metadata and raw FastQ files from public databases
nf-core/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
dockstore/dockstore
Our VM/Docker sharing infrastructure and management component
lynnlangit/aws-for-bioinformatics
AWS for Bioinformatics Researchers
nf-core/viralrecon
Assembly and intrahost/low-frequency variant calling for viral samples
EBI-Metagenomics/emg-viral-pipeline
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
nextflow-io/training
Nextflow training material
PGScatalog/pgsc_calc
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
replikation/What_the_Phage
WtP: Phage identification via nextflow and docker or singularity
fmalmeida/bacannot
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
stevekm/nextflow-demos
Example Nextflow pipelines and programming techniques
nf-core/test-datasets
Test data to be used for automated testing with the nf-core pipelines