Workflows
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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
Downloadnf-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. ...
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 ...
Type: Nextflow
Creator: Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry
Submitter: Finn Bacall
Introduction
nfcore/ampliseq is a bioinformatics analysis pipeline used for 16S rRNA amplicon sequencing data.
The workflow processes raw data from FastQ inputs (FastQC), trims primer sequences from the reads (Cutadapt), imports data into QIIME2, generates amplicon sequencing variants (ASV, DADA2), classifies features against the SILVA v132 database, excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta ...
