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A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html
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RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
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Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
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YAMP: Yet Another Metagenomic Pipeline
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See the main fork of this repository here >>>
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Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
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16S rRNA amplicon sequencing analysis workflow using QIIME2
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GATK RNA-Seq Variant Calling in Nextflow
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RNA-seq analysis pipeline for detection gene-fusions
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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
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A proof of concept RNA-Seq pipeline with Nextflow
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Google's DeepVariant variant caller as a Nextflow pipeline
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DEPRECIATED! Please use nf-core/tools instead
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Example Nextflow pipelines and programming techniques
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A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools
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ATAC-seq peak-calling and differential analysis pipeline.
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A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
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🔬 De novo assembly of nanopore reads using nextflow -
Nextflow basic tutorial for newbie users
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Deep Variant as a Nextflow pipeline
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RNA mapping pipeline
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A fully reproducible and state of the art ancient DNA analysis pipeline.
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UNDER DEVELOPMENT--- A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
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CAMITAX: Taxon labels for microbial genomes
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Nextflow workshop 2018 -- Training pages -> https://nextflow-io.github.io/nf-hack18/
