Search Results - RepositoryStats

680

2.9k

apache-2.0

88

A DSL for data-driven computational pipelines

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

Created 2013-03-27

6,992 commits to master branch, last one 3 days ago

rnaseq nf-core

747

1.0k

mit

175

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

rna nf-core rna-seq nextflow pipeline workflow

Created 2018-03-29

5,806 commits to master branch, last one 4 months ago

awesome-nextflow nextflow-io

89

586

cc0-1.0

32

A curated list of nextflow based pipelines

nextflow awesome-list

Created 2015-07-27

152 commits to master branch, last one 2 years ago

bactopia bactopia

76

454

mit

16

A flexible pipeline for complete analysis of bacterial genomes

conda fastqs bioconda nextflow bacterial-genomes

Created 2019-02-22

1,632 commits to master branch, last one about a month ago

sarek nf-core

440

441

mit

151

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

Created 2019-04-30

7,941 commits to master branch, last one 2 months ago

modules nf-core

837

354

mit

215

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

dsl2 modules nf-core nf-test nextflow pipelines workflows

Created 2019-07-26

7,230 commits to master branch, last one 2 days ago

patterns nextflow-io

71

346

mit

24

A curated collection of Nextflow implementation patterns

nextflow

Created 2015-02-05

107 commits to master branch, last one about a year ago

scrnaseq nf-core

187

263

mit

154

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics

Created 2019-04-08

1,761 commits to master branch, last one about a month ago

gcp-for-bioinformatics lynnlangit

70

259

apache-2.0

15

GCP for Bioinformatics Researchers

gcp google genomics nextflow google-batch bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers

Created 2019-06-06

1,222 commits to master branch, last one 4 months ago

tools nf-core

201

256

mit

168

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

linter python linting nf-core nextflow pipeline workflow bioinformatics

Created 2018-02-13

12,120 commits to main branch, last one 2 months ago

mag nf-core

124

233

mit

179

Assembly and binning of metagenomes

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

Created 2018-05-22

2,659 commits to master branch, last one 16 days ago

npm-groovy-lint nvuillam

64

219

mit

5

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

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

Created 2020-02-13

448 commits to main branch, last one about a month ago

chipseq nf-core

151

211

mit

165

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

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

Created 2018-04-24

1,835 commits to master branch, last one 6 months ago

atacseq nf-core

125

200

mit

167

ATAC-seq peak-calling and QC analysis pipeline

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

Created 2018-11-05

1,416 commits to master branch, last one about a year ago

ampliseq nf-core

134

199

mit

168

Amplicon sequencing analysis workflow using DADA2 and QIIME2

16s 18s its edna rrna pacbio qiime2 nf-core illumina nextflow pipeline workflow iontorrent microbiome metagenomics metabarcoding amplicon-sequencing taxonomic-profiling taxonomic-classification

Created 2018-09-26

2,715 commits to master branch, last one 20 days ago

nanoseq nf-core

93

198

mit

154

Nanopore demultiplexing, QC and alignment pipeline

qc nf-core nanopore nextflow pipeline workflow alignment demultiplexing

Created 2019-09-09

1,587 commits to master branch, last one 2 years ago

fetchngs nf-core

80

174

mit

117

Pipeline to fetch metadata and raw FastQ files from public databases

ena geo sra ddbj fastq nf-core synapse download nextflow pipeline workflow

Created 2021-06-03

1,079 commits to master branch, last one about a year ago

methylseq nf-core

153

165

mit

169

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

pbat rrbs em-seq nf-core nextflow pipeline workflow epigenome methyl-seq epigenomics dna-methylation bisulfite-sequencing

Created 2018-03-12

1,691 commits to master branch, last one 4 months ago

eager nf-core

83

162

mit

177

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

adna genome nf-core nextflow pipeline workflow ancientdna metagenomics bioinformatics pathogen-genomics population-genetics ancient-dna-analysis

Created 2018-06-03

3,279 commits to master branch, last one about a month ago

training nextflow-io

194

162

other

10

Nextflow training material

learning nextflow teaching training tutorial workshop pipelines workflows

Created 2020-08-27

2,373 commits to master branch, last one 2 days ago

nf-test askimed

27

159

mit

7

Simple test framework for Nextflow pipelines

testing nextflow testing-tools test-automation

Created 2021-10-18

391 commits to main branch, last one 4 months ago

rnafusion nf-core

110

153

mit

166

RNA-seq analysis pipeline for detection of gene-fusions

rna fusion nf-core rna-seq nextflow pipeline workflow gene-fusion fusion-genes

Created 2018-10-05

1,913 commits to master branch, last one 3 months ago

nf-tower seqeralabs

55

150

mpl-2.0

17

Nextflow Tower system

nextflow

This repository has been archived (exclude archived)

Created 2019-04-15

873 commits to master branch, last one 2 months ago

aws-for-bioinformatics lynnlangit

35

145

apache-2.0

8

AWS for Bioinformatics Researchers

aws ec2 athena awsbatch genomics nextflow aws-batch sagemaker bioinformatics

Created 2022-03-29

507 commits to main branch, last one 8 months ago

taxprofiler nf-core

49

144

mit

172

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

nf-core shotgun illumina nanopore nextflow pathogen pipeline workflow profiling long-reads microbiome metagenomics bioinformatics classification taxonomic-profiling taxonomic-classification

Created 2022-02-18

2,145 commits to master branch, last one about a month ago

viralrecon nf-core

128

137

mit

124

Assembly and intrahost/low-frequency variant calling for viral samples

ont artic viral virus covid19 nf-core amplicon assembly covid-19 illumina nanopore nextflow pipeline workflow sars-cov-2 metagenomics oxford-nanopore variant-calling long-read-sequencing

Created 2020-03-30

2,788 commits to master branch, last one 2 years ago