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+ @article{koster_snakemakescalablebioinformaticsworkflow_2012, title={Snakemake—a scalable bioinformatics workflow engine}, volume={28}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/bts480}, DOI={10.1093/bioinformatics/bts480}, number={19}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Köster, Johannes and Rahmann, Sven}, year={2012}, month=aug, pages={2520–2522} }
+
+ @article{amezquita_orchestratingsinglecell_2020, title={Orchestrating single-cell analysis with Bioconductor}, volume={17}, ISSN={1548-7105}, url={http://dx.doi.org/10.1038/s41592-019-0654-x}, DOI={10.1038/s41592-019-0654-x}, number={2}, journal={Nature Methods}, publisher={Springer Science and Business Media LLC}, author={Amezquita, Robert A. and Lun, Aaron T. L. and Becht, Etienne and Carey, Vince J. and Carpp, Lindsay N. and Geistlinger, Ludwig and Marini, Federico and Rue-Albrecht, Kevin and Risso, Davide and Soneson, Charlotte and Waldron, Levi and Pagès, Hervé and Smith, Mike L. and Huber, Wolfgang and Morgan, Martin and Gottardo, Raphael and Hicks, Stephanie C.}, year={2019}, month=dec, pages={137–145} }
+
+ @article{huemos_bestpracticessingle_2023, title={Best practices for single-cell analysis across modalities}, volume={24}, ISSN={1471-0064}, url={http://dx.doi.org/10.1038/s41576-023-00586-w}, DOI={10.1038/s41576-023-00586-w}, number={8}, journal={Nature Reviews Genetics}, publisher={Springer Science and Business Media LLC}, author={Heumos, Lukas and Schaar, Anna C. and Lance, Christopher and Litinetskaya, Anastasia and Drost, Felix and Zappia, Luke and Lücken, Malte D. and Strobl, Daniel C. and Henao, Juan and Curion, Fabiola and Aliee, Hananeh and Ansari, Meshal and Badia-i-Mompel, Pau and Büttner, Maren and Dann, Emma and Dimitrov, Daniel and Dony, Leander and Frishberg, Amit and He, Dongze and Hediyeh-zadeh, Soroor and Hetzel, Leon and Ibarra, Ignacio L. and Jones, Matthew G. and Lotfollahi, Mohammad and Martens, Laura D. and Müller, Christian L. and Nitzan, Mor and Ostner, Johannes and Palla, Giovanni and Patro, Rob and Piran, Zoe and Ramírez-Suástegui, Ciro and Saez-Rodriguez, Julio and Sarkar, Hirak and Schubert, Benjamin and Sikkema, Lisa and Srivastava, Avi and Tanevski, Jovan and Virshup, Isaac and Weiler, Philipp and Schiller, Herbert B. and Theis, Fabian J.}, year={2023}, month=mar, pages={550–572} }
+
+ @article{luecken_currentbestpractices_2019, title={Current best practices in single‐cell RNA‐seq analysis: a tutorial}, volume={15}, ISSN={1744-4292}, url={http://dx.doi.org/10.15252/msb.20188746}, DOI={10.15252/msb.20188746}, number={6}, journal={Molecular Systems Biology}, publisher={EMBO}, author={Luecken, Malte D and Theis, Fabian J}, year={2019}, month=jun }
+
+ @article{nfcoreframeworkcommunity_ewels2020, title={The nf-core framework for community-curated bioinformatics pipelines}, volume={38}, ISSN={1546-1696}, url={http://dx.doi.org/10.1038/s41587-020-0439-x}, DOI={10.1038/s41587-020-0439-x}, number={3}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Ewels, Philip A. and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven}, year={2020}, month=feb, pages={276–278} }
+
+ @article{ditommaso_nextflowenablesreproducible_2017, title={Nextflow enables reproducible computational workflows}, volume={35}, ISSN={1546-1696}, url={http://dx.doi.org/10.1038/nbt.3820}, DOI={10.1038/nbt.3820}, number={4}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric}, year={2017}, month=apr, pages={316–319} }
+
+@misc{avantika_lal_2021_4638196,
+  doi = {10.5281/ZENODO.4638196},
+  url = {https://zenodo.org/record/4638196},
+  author = {Lal, Avantika and Nolet, Corey J. and Ilango, Rajesh and Movva, Raj},
+  title = {clara-parabricks/rapids-single-cell-examples: v2021.03.0},
+  publisher = {Zenodo},
+  year = {2021},
+  copyright = {Open Access}
+}
+
+@inproceedings{luecken_sandboxpredictionintegration_2021,
+  title={A sandbox for prediction and integration of {DNA}, {RNA}, and proteins in single cells},
+  author={Malte D Luecken and Daniel Bernard Burkhardt and Robrecht Cannoodt and Christopher Lance and Aditi Agrawal and Hananeh Aliee and Ann T Chen and Louise Deconinck and Angela M Detweiler and Alejandro A Granados and Shelly Huynh and Laura Isacco and Yang Joon Kim and Dominik Klein and BONY DE KUMAR and Sunil Kuppasani and Heiko Lickert and Aaron McGeever and Honey Mekonen and Joaquin Caceres Melgarejo and Maurizio Morri and Michaela M{\"u}ller and Norma Neff and Sheryl Paul and Bastian Rieck and Kaylie Schneider and Scott Steelman and Michael Sterr and Daniel J. Treacy and Alexander Tong and Alexandra-Chloe Villani and Guilin Wang and Jia Yan and Ce Zhang and Angela Oliveira Pisco and Smita Krishnaswamy and Fabian J Theis and Jonathan M. Bloom},
+  booktitle={Thirty-fifth Conference on Neural Information Processing Systems Datasets and Benchmarks Track (Round 2)},
+  year={2021},
+  url={https://openreview.net/forum?id=gN35BGa1Rt}
+}
+
+@article{merkel_dockerlightweight_2014,
+  title={Docker: lightweight linux containers for consistent development and deployment},
+  author={Merkel, Dirk},
+  journal={Linux journal},
+  volume={2014},
+  number={239},
+  pages={2},
+  year={2014}
+}
+
+@misc{heon_podmantoolmanaging_2018,
+  doi = {10.5281/ZENODO.4735634},
+  url = {https://zenodo.org/record/4735634},
+  author = {Heon, Matt et. al and Walsh, Dan and Baude, Brent and Mohnani, Urvashi and Cui, Ashley and Sweeney, Tom and Scrivano, Giuseppe and Evich, Chris and Rothberg, Valentin and Trmač, Miloslav and Honce, Jhon and Wang, Qi and Mandvekar, Lokesh and Reber, Adrian and Santiago, Eduardo and Grunert, Sascha and Dahyabhai, Nalin and Bjorklund, Anders and Kushwaha, Kunal and Ashwin Sha, Sujil and Pu, Yiqiao and {Zhangguanzhang} and Vasek, Matej and {Podman Community}},
+  keywords = {Podman, OpenSource, HPC, Containers, OCI, kubernetes},
+  language = {en},
+  title = {Podman - : A tool for managing OCI containers and pods},
+  publisher = {Zenodo},
+  year = {2018},
+  copyright = {Creative Commons Attribution 4.0 International}
+}
+
+ @article{kurtzer_singularityscientificcontainers_2017, title={Singularity: Scientific containers for mobility of compute}, volume={12}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0177459}, DOI={10.1371/journal.pone.0177459}, number={5}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Kurtzer, Gregory M. and Sochat, Vanessa and Bauer, Michael W.}, editor={Gursoy, Attila}, year={2017}, month=may, pages={e0177459} }
+