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apetkau committed Jan 26, 2024
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# Acknowledgements

This pipeline uses code and infrastructure developed and maintained by the [nf-core][nf-core] initative, and reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

> The nf-core framework for community-curated bioinformatics pipelines.
>
> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
>
> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
In addition, references of tools and data used in this pipeline are as follows:

* The [fastq_download_prefetch_fasterqdump_sratools](https://nf-co.re/subworkflows/fastq_download_prefetch_fasterqdump_sratools) subworkflow from nf-core. Custom modifications to this workflow (and underlying modules) are found in the [subworkflows/local](subworkflows/local) and [modules/local](modules/local) directories.
- The [fastq_download_prefetch_fasterqdump_sratools](https://nf-co.re/subworkflows/fastq_download_prefetch_fasterqdump_sratools) subworkflow from nf-core. Custom modifications to this workflow (and underlying modules) are found in the [subworkflows/local](subworkflows/local) and [modules/local](modules/local) directories.

Other works this pipeline makes use of are found in the [CITATIONS.md](CITATIONS.md) file.

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