flomicsbiotech/sarscov2 repository overview

Workflow to diagnose SARSCoV2.

⁠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.

⁠Quick Start

i. Install nextflow⁠

ii. Install either Docker⁠ or Singularity⁠ for full pipeline reproducibility (please only use Conda⁠ as a last resort

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run Flomics/SARSCoV2 -profile test,<docker/singularity/conda/institute>

iv. Start running your own analysis!

nextflow run Flomics/SARSCoV2 -profile <docker/singularity/conda/institute> --input 'path/to/samplesheet/samplesheet.csv --protocol <amplicon/metagenomic> --kit <artic_v1/artic_v2/artic_v3/qiagen/swiftbio>'

nextflow run Flomics/SARSCoV2 -profile <docker/singularity/conda/awsbatch> --input 'path/to/samplesheet/samplesheet.csv' --protocol <amplicon/metagenomic> --kit <artic_v1/artic_v2/artic_v3/qiagen/swiftbio> --kraken2_db 'path/to/database/database.tar.gz'

nextflow run Flomics/SARSCoV2 -profile <docker/singularity/conda/awsbatch> --input 'path/to/samplesheet/samplesheet.csv' --protocol <amplicon/metagenomic> --kit <artic_v1/artic_v2/artic_v3/qiagen/swiftbio> --kraken2_db 'path/to/database'

See usage docs⁠ for all of the available options when running the pipeline.

⁠Documentation

The Flomics/SARSCoV pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Running the pipeline⁠
2. Output and how to interpret the results⁠

⁠Credits

Flomics/SARSCoV2 was originally written by Flomics bioinformatician team (Marta Pozuelo, Lluc Cabús and Joao Curado).

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch by mail⁠