Assembly and annotation of prokaryotic metatranscriptomes..
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.
i. Install nextflow
ii. Install one of docker, singularity or conda
iii. Download the pipeline and test it on a minimal dataset with a single command
nextflow run nf-core/metatdenovo -profile test,<docker/singularity/conda>iv. Start running your own analysis!
nextflow run nf-core/metatdenovo -profile <docker/singularity/conda> --reads '*_R{1,2}.fastq.gz' --genome GRCh37See usage docs for all of the available options when running the pipeline.
The nf-core/metatdenovo pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
nf-core/metatdenovo was originally written by daniel.lundin@lnu.se.
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 Slack (you can join with this invite).
You can cite the nf-core pre-print as follows:
Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.