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