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

    Nextflow 106 24 Built by @pditommaso @alperyilmaz @Bioninbo @davidmasp @mfoll
  2. RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

    Nextflow 103 110 Built by @ewels @Hammarn @apeltzer @Galithil @rfenouil
  3. Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

    Nextflow 97 76 Built by @MaxUlysse @szilvajuhos @marcelm @alneberg @pallolason
  4. YAMP: Yet Another Metagenomic Pipeline

    Nextflow 32 13 Built by @alesssia @pditommaso
  5. UNDER CONSTRUCTION: ChIP-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 29 36 Built by @chuan-wang @ewels @drpatelh @apeltzer @tiagochst
  6. See the main fork of this repository here >>>

    Nextflow 29 110 Built by @ewels @Hammarn @apeltzer @Galithil @rfenouil
  7. 16S rRNA amplicon sequencing analysis workflow using QIIME2

    Nextflow 26 15 Built by @apeltzer @d4straub
  8. GATK RNA-Seq Variant Calling in Nextflow

    Nextflow 26 15 Built by @pditommaso @emi80 @evanfloden @anvlasova
  9. RNA-seq analysis pipeline for detection gene-fusions

    Nextflow 25 17 Built by @matq007 @Hammarn @ewels @MaxUlysse @mtstahl
  10. Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

    Nextflow 24 44 Built by @ewels @Hammarn @apeltzer @phue @sven1103
  11. A proof of concept RNA-Seq pipeline with Nextflow

    Nextflow 21 22 Built by @pditommaso @vsoch
  12. Example Nextflow pipelines and programming techniques

    Nextflow 20 3 Built by @stevekm @pditommaso
  13. Google's DeepVariant variant caller as a Nextflow pipeline

    Nextflow 20 15 Built by @PhilPalmer @luisas @apeltzer @MaxUlysse @ewels
  14. ATAC-seq peak-calling, QC and differential analysis pipeline.

    Nextflow 20 7 Built by @drpatelh @ewels @apeltzer
  15. DEPRECIATED! Please use nf-core/tools instead

    Nextflow 19 7 Built by @ewels @apeltzer @sven1103 @alneberg @MaxUlysse
  16. A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

    Nextflow 18 15 Built by @evanfloden @pditommaso
  17. A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

    Nextflow 18 6 Built by @anfederico @montilab
  18. 🔬 De novo assembly of nanopore reads using nextflow

    Nextflow 17 2 Built by @HadrienG @alesssia @shaze @jhayer
  19. Nextflow basic tutorial for newbie users

    Nextflow 17 8 Built by @pditommaso @evanfloden
  20. Deep Variant as a Nextflow pipeline

    Nextflow 17 15 Built by @luisas @PhilPalmer @pprieto @mariach
  21. A fully reproducible and state of the art ancient DNA analysis pipeline.

    Nextflow 16 21 Built by @apeltzer @jfy133 @maxibor @phue @evanfloden
  22. RNA mapping pipeline

    Nextflow 16 4 Built by @pditommaso @pprieto
  23. UNDER DEVELOPMENT--- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets

    Nextflow 12 24 Built by @likelet @bioinformatist @sateeshperi @kodayu @apeltzer
  24. CAMITAX: Taxon labels for microbial genomes

    Nextflow 11 1 Built by @abremges @pditommaso
  25. Nextflow workshop 2018 -- Training pages -> https://nextflow-io.github.io/nf-hack18/

    Nextflow 11 3 Built by @pditommaso @emi80 @evanfloden @damjanaram
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