nextflow

Here are 507 public repositories matching this topic...

nextflow-io / nextflow

A DSL for data-driven computational pipelines

docker groovy hello aws cloud bioinformatics pipeline nextflow hpc reproducible-research workflow-engine slurm pipeline-framework sge singularity reproducible-science dataflow singularity-containers

Updated Sep 15, 2022
Groovy

nf-core / rnaseq

Star

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

workflow rna-seq pipeline nextflow rna nf-core

Updated Sep 1, 2022
Nextflow

nextflow-io / awesome-nextflow

Star

A curated list of nextflow based pipelines

nextflow awesome-list

Updated Jun 6, 2022

nextflow-io / patterns

Star

A curated collection of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html

nextflow

Updated Sep 6, 2022
Nextflow

assemblerflow / flowcraft

Star

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳

📦

pipeline genomics nextflow bacterial

Updated May 11, 2020
Python

nf-core / sarek

Star

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Updated Sep 15, 2022
Nextflow

bactopia / bactopia

Star

A flexible pipeline for complete analysis of bacterial genomes

nextflow conda bioconda bacterial-genomes fastqs

Updated Aug 3, 2022
Nextflow

nf-core / tools

Star

Python package with helper tools for the nf-core community.

python workflow bioinformatics pipeline nextflow linting linter nf-core

Updated Sep 15, 2022
Python

SciLifeLab / Sarek

Star

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

docker workflow bioinformatics pipeline genomics nextflow cancer somatic-variants reproducible-research containers next-generation-sequencing singularity reproducible-science somatic germline germline-variants

Updated Jan 27, 2020
Nextflow

nf-core / chipseq

Star

ChIP-seq peak-calling, QC and differential analysis pipeline.

workflow pipeline nextflow chip chip-seq macs2 nf-core chromatin-immunoprecipitation peak-calling

Updated Sep 15, 2022
Nextflow

nf-core / modules

Star

Repository to host tool-specific module files for the Nextflow DSL2 community!

modules nextflow pipelines workflows nf-core dsl2

Updated Sep 15, 2022
Nextflow

nf-core / atacseq

Star

ATAC-seq peak-calling, QC and differential analysis pipeline

workflow pipeline nextflow atac-seq nf-core chromatin-accessibiity

Updated Sep 1, 2022
Nextflow

seqeralabs / nf-tower

Star

Nextflow Tower system

nextflow

Updated Sep 8, 2022
Groovy

nvuillam / npm-groovy-lint

Sponsor

Star

Lint, format and auto-fix your Groovy / Jenkinsfile / Gradle files using command line

lint groovy gradle nextflow ci groovy-language linter codenarc jenkinsfile sarif code-quality-analyzer sarif-report megalinter

Updated Aug 15, 2022
JavaScript

nf-core / mag

Star

Assembly and binning of metagenomes

workflow bioinformatics nanopore pipeline annotation nextflow assembly metagenomics binning metagenomes nanopore-sequencing nf-core long-read-sequencing

Updated Sep 1, 2022
Nextflow

dockstore / dockstore

Star

Our VM/Docker sharing infrastructure and management component

docker workflow bioinformatics nextflow containers wdl cwl dockstore

Updated Sep 15, 2022
Java

CRG-CNAG / CalliNGS-NF

Star

GATK RNA-Seq Variant Calling in Nextflow

bioinformatics rna-seq genomics nextflow ngs gatk variant-calling

Updated Aug 25, 2021
Nextflow

nf-core / ampliseq

Star

Amplicon sequencing analysis workflow using DADA2 and QIIME2

workflow pipeline nextflow metagenomics 16s qiime rrna amplicon-sequencing nf-core

Updated Sep 15, 2022
Nextflow

UMMS-Biocore / dolphinnext

Star

A graphical user interface for distributed data processing of high throughput genomics

bioinformatics rna-seq pipeline nextflow drag-and-drop pipelines chip-seq atac-seq clusters workflows amazon-cloud dolphinnext share-pipelines

Updated Sep 14, 2022
PHP

nf-core / methylseq

Star

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

workflow pipeline nextflow dna-methylation methyl-seq bisulfite-sequencing nf-core

Updated Sep 15, 2022
Nextflow

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