nf-core

Repositories

• proteomicslfq

  Proteomics label-free quantification (LFQ) analysis pipeline

  workflow pipeline nextflow proteomics openms label-free-quantification nf-core
  Nextflow MIT 13 11 16 (2 issues need help) 3 Updated Nov 11, 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 5 1 1 2 Updated Nov 11, 2020

• pangenome

  Forked from subwaystation/pangenome

  Renders a collection of sequences into a pangenome graph.

  workflow pipeline nextflow pangenome nf-core
  Nextflow MIT 2 4 0 3 Updated Nov 11, 2020

• rnaseq

  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
  Nextflow MIT 251 231 17 (1 issue needs help) 1 Updated Nov 11, 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 64 22 1 4 Updated Nov 11, 2020

• nanoseq

  Nanopore demultiplexing, QC and alignment pipeline

  workflow nanopore pipeline nextflow alignment qc demultiplexing
  Nextflow MIT 16 21 5 1 Updated Nov 11, 2020

• methylseq

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

  workflow pipeline nextflow dna-methylation methyl-seq bisulfite-sequencing nf-core
  Nextflow MIT 64 50 13 (1 issue needs help) 4 Updated Nov 11, 2020

• smrnaseq

  A small-RNA sequencing analysis pipeline

  workflow pipeline nextflow small-rna nf-core smrna-seq
  Nextflow MIT 42 14 12 0 Updated Nov 11, 2020

• tools

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

  python workflow bioinformatics pipeline nextflow linting linter
  Python MIT 53 80 48 4 Updated Nov 11, 2020

• testpipeline

  A small example pipeline used to test new nf-core infrastructure and common code.
  Nextflow MIT 1 0 0 0 Updated Nov 11, 2020

• ampliseq

  16S rRNA amplicon sequencing analysis workflow using QIIME2

  workflow pipeline nextflow metagenomics 16s qiime rrna
  Nextflow MIT 32 49 9 0 Updated Nov 11, 2020

• configs

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

  bioinformatics nextflow configuration pipelines workflows nf-core
  Nextflow MIT 44 17 5 9 Updated Nov 11, 2020

• mag

  Assembly and binning of metagenomes

  workflow bioinformatics pipeline annotation nextflow assembly metagenomics
  Nextflow MIT 19 26 11 0 Updated Nov 10, 2020

• nf-co.re

  Code and files for the main nf-core website.

  website nextflow nf-core
  PHP MIT 55 21 37 (1 issue needs help) 4 Updated Nov 10, 2020

• eager

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

  workflow bioinformatics pipeline genome nextflow metagenomics population-genetics
  Nextflow MIT 36 37 20 (2 issues need help) 0 Updated Nov 9, 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 Nov 8, 2020

• hic

  Analysis of Chromosome Conformation Capture data (Hi-C)

  workflow pipeline nextflow hi-c chromosome-conformation-capture nf-core
  Python MIT 18 20 15 0 Updated Nov 7, 2020

• sarek

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

  docker workflow bioinformatics pipeline genomics nextflow cancer
  Nextflow MIT 138 75 38 8 Updated Nov 7, 2020

• kmermaid

  k-mer similarity analysis pipeline

  workflow pipeline nextflow kmer k-mer kmer-frequency-count kmer-counting
  Nextflow MIT 9 6 10 5 Updated Nov 5, 2020

• bacass

  Simple bacterial assembly and annotation pipeline

  workflow pipeline nextflow genome-assembly bacterial-genomes nf-core
  Nextflow MIT 14 15 2 (1 issue needs help) 0 Updated Nov 5, 2020

• dualrnaseq

  Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.

  workflow rna-seq pipeline nextflow quantification nf-core host-pathogen
  Nextflow MIT 2 0 0 0 Updated Nov 3, 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 24 31 7 (1 issue needs help) 1 Updated Oct 28, 2020

• imcyto

  Image Mass Cytometry analysis pipeline

  workflow pipeline nextflow image-processing image-segmentation image-analysis cytometry
  Python MIT 7 7 1 0 Updated Oct 27, 2020

• chipseq

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

  workflow pipeline nextflow chip chip-seq macs2 nf-core
  Nextflow MIT 65 62 6 0 Updated Oct 27, 2020

• atacseq

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

  workflow pipeline nextflow atac-seq nf-core chromatin-accessibiity
  Nextflow MIT 42 54 8 (1 issue needs help) 0 Updated Oct 27, 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 25 6 1 Updated Oct 27, 2020

• scrnaseq

  A single-cell RNAseq pipeline for 10X genomics data

  workflow pipeline nextflow nf-core
  Nextflow MIT 16 14 14 (1 issue needs help) 2 Updated Oct 27, 2020

• slamseq

  Forked from t-neumann/slamseq

  SLAMSeq processing and analysis pipeline

  workflow pipeline nextflow slamseq transcriptomics differential-expression nf-core
  Nextflow MIT 7 3 4 1 Updated Oct 27, 2020

• smartseq2

  Forked from icbi-lab/smartseq2_pipeline

  A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

  workflow pipeline nextflow nf-core
  Nextflow MIT 5 5 0 2 Updated Oct 27, 2020

• metaboigniter

  Forked from MetaboIGNITER/metaboigniter

  UNDER CONSTRUCTION: MetaboIGNITER - Get your metabolomics analysis up and running

  workflow pipeline nextflow identification metabolomics mass-spectrometry quantification
  HTML MIT 2 0 0 1 Updated Oct 27, 2020