Workflows

nf-core/clinvap

Clinical Variant Annotation Pipeline

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/clinvap pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local installation Adding your own system ...

nf-core/crisprvar

Run CRISPResso on genome editing experiments

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/crisprvar pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local installation Adding ...

nf-core/ddamsproteomics

Quantitative shotgun MS proteomics as done in Lehtio lab

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/ddamsproteomics pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local ...

nf-core/deepvariant

Deep Variant as a Nextflow pipeline

A Nextflow pipeline for running the Google DeepVariant variant caller.

What is DeepVariant and why in Nextflow?

The Google Brain Team in December 2017 released a Variant Caller based on DeepLearning: DeepVariant.

In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format. ...

Hybrid genome assembly.

Introduction

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Documentation

The nf-core/denovohybrid pipeline comes with documentation about the pipeline, found in the docs/ directory:

Installation Pipeline configuration

Local installation Adding your own system config Reference genomes

Running the ...

Automated quantitative analysis of DIA proteomics mass spectrometry measurements.

Introduction

nfcore/diaproteomics is a bioinformatics analysis pipeline used for quantitative processing of data independant (DIA) proteomics data.

The workflow is based on the OpenSwathWorkflow for SWATH-MS proteomic data. DIA RAW files (mzML) serve as inputs and library search is performed based on a given input spectral library. If specified internal retention time standarts (irts) will be used to align library ...

A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support..

Introduction

nf-core/eager is a bioinformatics best-practice analysis pipeline for NGS sequencing based ancient DNA (aDNA) data analysis.

The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FASTQ inputs, aligns the reads and performs extensive general NGS and aDNA specific quality-control on the results. It comes with docker, singularity or conda containers making ...