nf-core

Repositories

• eager

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

  workflow bioinformatics pipeline genome nextflow metagenomics population-genetics
  Nextflow 32 34 22 (2 issues need help) 3 Updated Sep 25, 2020

• clinvap Archived

  Forked from sbilge/nf-core-clinvap

  WIP: A Nextflow pipeline to perform clinical variant annotation and reporting

  workflow pipeline annotation nextflow clinical variant-annotation nf-core
  Nextflow MIT 4 8 1 1 Updated Sep 25, 2020

• mag

  Assembly and binning of metagenomes

  workflow bioinformatics pipeline annotation nextflow assembly metagenomics
  Nextflow MIT 18 24 11 1 Updated Sep 25, 2020

• nf-co.re

  Code and files for the main nf-core website.

  website nextflow nf-core
  PHP MIT 52 20 32 (1 issue needs help) 2 Updated Sep 25, 2020

• diaproteomics

  Forked from Leon-Bichmann/diaproteomics

  Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

  workflow pipeline nextflow proteomics openms nf-core data-independent-proteomics
  Nextflow MIT 4 1 5 0 Updated Sep 25, 2020

• mhcquant

  Forked from Leon-Bichmann/MHCquant

  Identify and quantify MHC eluted peptides from mass spectrometry raw data

  workflow pipeline nextflow mhc mass-spectrometry openms peptides
  Nextflow MIT 14 12 0 1 Updated Sep 25, 2020

• rnafusion

  RNA-seq analysis pipeline for detection gene-fusions

  workflow rna-seq pipeline nextflow gene-fusion fusion rna
  Nextflow MIT 34 49 5 1 Updated Sep 25, 2020

• test-datasets

  Test data to be used for automated testing with the nf-core pipelines

  testing workflow nextflow pipelines test-data test-datasets nf-core
  MIT 60 17 1 5 Updated Sep 25, 2020

• epitopeprediction

  A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

  workflow pipeline nextflow epitope-prediction nf-core epitope mhc-binding-prediction
  Python MIT 8 6 1 0 Updated Sep 24, 2020

• sarek

  Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

  docker workflow bioinformatics pipeline genomics nextflow cancer
  Nextflow MIT 129 66 35 3 Updated Sep 22, 2020

• bcellmagic

  B cell repertoire sequencing analysis pipeline using the immcantation framework

  workflow pipeline nextflow nf-core b-cell repseq immcantation
  Nextflow MIT 10 10 4 1 Updated Sep 21, 2020

• rnaseq

  RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control

  workflow rna-seq pipeline nextflow rna nf-core
  Nextflow MIT 238 217 14 0 Updated Sep 18, 2020

• modules

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

  modules nextflow pipelines workflows nf-core dsl2
  1 package HTML MIT 20 24 5 (1 issue needs help) 0 Updated Sep 18, 2020

• configs

  Config files used to define parameters specific to compute environments at different Institutions

  bioinformatics nextflow configuration pipelines workflows nf-core
  Nextflow MIT 41 16 5 7 Updated Sep 16, 2020

• neutronstar Archived

  De novo assembly pipeline for 10X linked-reads using Supernova

  workflow pipeline nextflow genome-assembly denovo-assembly 10x-genomics 10xgenomics
  Nextflow MIT 6 3 0 0 Updated Sep 15, 2020

• kmermaid

  k-mer similarity analysis pipeline

  workflow pipeline nextflow kmer k-mer kmer-frequency-count kmer-counting
  Nextflow MIT 8 5 13 (1 issue needs help) 5 Updated Sep 15, 2020

• proteomicslfq

  UNDER CONSTRUCTION - Proteomics label-free quantification (LFQ) analysis pipeline

  workflow pipeline nextflow proteomics openms label-free-quantification nf-core
  Nextflow MIT 12 8 12 (2 issues need help) 3 Updated Sep 12, 2020

• bacass

  Simple bacterial assembly and annotation pipeline

  workflow pipeline nextflow genome-assembly bacterial-genomes nf-core
  Nextflow MIT 13 12 7 3 Updated Sep 8, 2020

• tools

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

  python workflow bioinformatics pipeline nextflow linting linter
  Python MIT 49 77 50 4 Updated Sep 4, 2020

• hic

  Analysis of Chromosome Conformation Capture data (Hi-C)

  workflow pipeline nextflow hi-c chromosome-conformation-capture nf-core
  Python MIT 17 20 15 0 Updated Sep 3, 2020

• nanoseq

  Nanopore demultiplexing, QC and alignment pipeline

  workflow nanopore pipeline nextflow alignment qc demultiplexing
  Nextflow MIT 16 18 9 0 Updated Aug 27, 2020

• cageseq

  CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.

  workflow pipeline nextflow gene-expression rna cage nf-core
  Nextflow MIT 5 2 0 1 Updated Aug 24, 2020

• hlatyping

  Precision HLA typing from next-generation sequencing data

  workflow pipeline nextflow dna rna immunology hla
  Nextflow MIT 18 17 4 (1 issue needs help) 1 Updated Aug 24, 2020

• PTM-Shepherd

  Forked from Nesvilab/PTM-Shepherd

  A tool for summarizing open search results
  Java 3 0 0 0 Updated Aug 22, 2020

• imcyto

  Image Mass Cytometry analysis pipeline

  workflow pipeline nextflow image-processing image-segmentation image-analysis cytometry
  Python MIT 7 7 0 0 Updated Aug 18, 2020

• viralrecon

  Forked from drpatelh/nf-core-viralrecon

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

  workflow virus pipeline nextflow assembly metagenomics variant-calling
  Nextflow MIT 20 23 6 1 Updated Aug 18, 2020

• chipseq

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

  workflow pipeline nextflow chip chip-seq macs2 nf-core
  Nextflow MIT 63 58 7 0 Updated Aug 18, 2020

• atacseq

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

  workflow pipeline nextflow atac-seq nf-core chromatin-accessibiity
  Nextflow MIT 38 48 8 (1 issue needs help) 0 Updated Aug 18, 2020

• gwas

  A pipeline for Genome Wide Association Studies

  workflow pipeline nextflow nf-core
  Nextflow MIT 5 2 0 1 Updated Aug 13, 2020

• awsmegatests

  CloudFormation templates to setup the aws megatests necessary cloud infrastructure
  Shell 2 3 3 0 Updated Aug 4, 2020