Workflows
What is a Workflow?Filters
Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community..
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.
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. ...
DownloadIdentify and quantify peptides from mass spectrometry raw data
Introduction
nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependant (DDA) peptidomics data.
It was specifically designed to analyse immunopeptidomics data, which deals with the analysis of affinity purified, unspecifically cleaved peptides that have recently been discussed intensively in the context of cancer vaccines.
The workflow is based on the OpenMS C++ framework for computational ...
nf-core/guideseq
Pipeline for GUIDE-Seq data analysis. Find off-target cleavage sites..
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/guideseq pipeline comes with documentation about the pipeline, found in the docs/ directory:
Installation Pipeline configuration
Local ...
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 ...
Type: Nextflow
Creator: Project author name (use a comma to separate multiple names).
Submitter: Finn Bacall
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 ...
Type: Nextflow
Creator: Project author name (use a comma to separate multiple names).
Submitter: Finn Bacall
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. ...
