CDCgov/aquascope is a bioinformatics best-practice pipeline for early detection of SARS-COV variants of concern, sequenced throughshotgun metagenomic sequencing, from wastewater.
This project is a successor to the C-WAP pipeline and is intended to process SARS-CoV-2 wastewater samples to determine relative variant abundance.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible.
- Read QC:
FastQC
- Trimming reads:
Fastp
- Aligning short reads:
Minimap2
- Ivar trim aligned reads:
IVAR Trim
- Freyja Variant classification:
Freyja
- Present QC for raw reads:
MultiQC
-
Install
Nextflow
(>=21.04.0
) -
Install any of
Docker
,Singularity
,Podman
,Shifter
orCharliecloud
for full pipeline reproducibility (please only useConda
as a last resort; see docs) -
Prepare the
assets/samplesheet.csv
. Refer to [prepare-files] (https://cdcgov.github.io/aquascope/). -
Prepare the configuration files A.
nextflow.config
is prepared with default parameters, update as needed B.test.config
is prepared with default parameters, update as needed C.cdc-dev.config
is prepared for CDC-Users and it has the Rosalind cluster configurations. -
Run the pipeline profile
nextflow run main.nf -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
A. The
-profile test
will run the test parameters and samples only for Illumina test data- Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>
in your command. This will enable eitherdocker
orsingularity
and set the appropriate execution settings for your local compute environment. NOTE: CDC users can only use singularity on SciComp resources. - If you are using
singularity
then the pipeline will auto-detect this and attempt to download the Singularity images directly. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the--singularity_pull_docker_container
parameter to pull and convert the Docker image instead. - If you are using
conda
, it is highly recommended to use theNXF_CONDA_CACHEDIR
orconda.cacheDir
settings to store the environments in a central location for future pipeline runs.
- Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
For more detailed documentation, please visit our user-guides.
Aquascope
was largely developed by OAMD's SciComp Team, with inputs from NWSS and the DCIPHER Team at Palantir. Detailed contributions can be found in our user-guides.
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 on the Slack #aquascope
channel (you can join with this invite).
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md
file.