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Detect germline or somatic variants from normal or tumour/normal whole-genome sequencing data
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A curated collections of Nextflow implementation patterns
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RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control
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See the main fork of this repository here >>>
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YAMP: Yet Another Metagenomic Pipeline
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Template for your own top-end Nextflow pipeline, customised using Cookiecutter
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A proof of concept RNA-Seq pipeline with Nextflow
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Nextflow basic tutorial for newbie users
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RNA mapping pipeline
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A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools
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Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
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Chromatin immunoprecipitation (ChIP-seq) analysis using BWA and MACS2 with QC steps.
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A flexible Nextflow-based framework for the definition of sequencing data processing pipelines
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Example Nextflow pipelines and programming techniques
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An automated ChIP-seq pipeline using Nextfow
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Deep Variant as a Nextflow pipeline
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🔬 De novo assembly of nanopore reads using nextflow -
WORK IN PROGRESS: Hopefully soon a fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.
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Exome Sequencing analysis pipeline (Work in progress)
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UNDER CONSTRUCTION: Assembly, binning and annotation of metagenomes.
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A Nextflow implementation of the Tuxedo Suite of Tools: HISAT, StringTie & Ballgown
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Documentation for Nextflow training at GCC/BOSC 2018
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Course on good practice in bioinformatics
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A Nextflow lncRNA Annotation Pipeline based on STAR, Cufflinks and FEELnc
