Search Results - RepositoryStats

605

2.6k

apache-2.0

85

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

6,521 commits to master branch, last one 6 days ago

rnaseq nf-core

673

802

mit

154

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

4,505 commits to master branch, last one 5 months ago

awesome-nextflow nextflow-io

90

556

cc0-1.0

33

A curated list of nextflow based pipelines

nextflow awesome-list

Created 2015-07-27

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

bactopia bactopia

64

373

mit

14

A flexible pipeline for complete analysis of bacterial genomes

conda fastqs bioconda nextflow bacterial-genomes

Created 2019-02-22

1,496 commits to master branch, last one 3 months ago

sarek nf-core

387

348

mit

129

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

Created 2019-04-30

7,370 commits to master branch, last one about a month ago

patterns nextflow-io

71

317

mit

24

A curated collection of Nextflow implementation patterns

nextflow

Created 2015-02-05

107 commits to master branch, last one 7 months ago

modules nf-core

650

258

mit

146

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

5,718 commits to master branch, last one 12 hours ago

gcp-for-bioinformatics lynnlangit

68

227

apache-2.0

14

GCP for Bioinformatics Researchers

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

Created 2019-06-06

1,162 commits to master branch, last one 3 days ago

tools nf-core

182

217

mit

143

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

linter python linting nf-core nextflow pipeline workflow bioinformatics

Created 2018-02-13

10,411 commits to master branch, last one about a month ago

npm-groovy-lint nvuillam

61

192

mit

6

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

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

mag nf-core

102

189

mit

157

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

2,180 commits to master branch, last one 16 days ago

chipseq nf-core

143

177

mit

144

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

1,542 commits to master branch, last one about a year ago

scrnaseq nf-core

154

177

mit

130

A single-cell RNAseq pipeline for 10X genomics data

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

Created 2019-04-08

1,401 commits to master branch, last one a day ago

atacseq nf-core

118

164

mit

146

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 10 months ago

ampliseq nf-core

107

162

mit

148

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

2,409 commits to master branch, last one 2 months ago

nanoseq nf-core

75

151

mit

134

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 about a year ago

nf-tower seqeralabs

51

143

mpl-2.0

17

Nextflow Tower system

nextflow

This repository has been archived (exclude archived)

Created 2019-04-15

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

methylseq nf-core

133

135

mit

147

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

1,297 commits to master branch, last one 5 months ago

rnafusion nf-core

92

130

mit

146

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

1,912 commits to master branch, last one 2 months ago

CalliNGS-NF CRG-CNAG

52

130

mpl-2.0

9

GATK RNA-Seq Variant Calling in Nextflow

ngs gatk rna-seq genomics nextflow bioinformatics variant-calling

Created 2017-02-28

171 commits to master branch, last one 2 years ago

nf-test askimed

17

127

mit

7

Simple test framework for Nextflow pipelines

testing nextflow testing-tools test-automation

Created 2021-10-18

370 commits to main branch, last one 19 days ago

fetchngs nf-core

69

127

mit

95

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 3 months ago

eager nf-core

78

127

mit

156

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

3,260 commits to master branch, last one 4 months ago

dockstore dockstore

27

116

apache-2.0

22

Our VM/Docker sharing infrastructure and management component

cwl wdl docker nextflow workflow dockstore containers bioinformatics

Created 2015-04-03

3,797 commits to develop branch, last one a day ago

viralrecon nf-core

103

111

mit

101

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 about a year ago

aws-for-bioinformatics lynnlangit

27

110

apache-2.0

7

AWS for Bioinformatics Researchers

aws ec2 athena awsbatch genomics nextflow aws-batch sagemaker bioinformatics

Created 2022-03-29

504 commits to main branch, last one 20 days ago

emg-viral-pipeline EBI-Metagenomics

13

109

apache-2.0

7

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

cwl viruses nextflow pipeline workflow

Created 2020-04-29

299 commits to master branch, last one about a month ago

training nextflow-io

104

108

other

8

Nextflow training material

learning nextflow teaching training tutorial workshop pipelines workflows

Created 2020-08-27

1,767 commits to master branch, last one 24 hours ago

taxprofiler nf-core

32

104

mit

148

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

1,784 commits to master branch, last one 6 days ago

pgsc_calc PGScatalog

18

104

apache-2.0

11

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

pgs prs nextflow workflow pgs-catalog polygenic-score polygenic-scores genetic-risk-score polygenic-risk-score polygenic-risk-scores

Created 2021-10-11

799 commits to main branch, last one 7 days ago