Cite in github readme Markdown - github

Question

I'm trying to get a publication on JOSS (journal open source software) and they require the paper written in markdown on github. I'm struggling in understanding how i can add the citation. So I included a file named paper.bib in my github main folder. In the Readme.md i wrote
---
title: 'CREDO: a friendly Customizable, REproducible, DOcker file generator'
tags:
- Docker
- Reproducibility
- Docker generator
- User Iinterface
authors:
- name: Simone Alessandri'
equal-contrib: 1
affiliation: 1
- name: Rabellino Sergio
equal-contrib: 2
affiliation: 2
- name: Sandro Contaldo
equal-contrib: 3
affiliation: 2
- name: Maria Ratto
equal-contrib: 3
affiliation: 4
- name: Gabriele Piacenti
equal-contrib: 3
affiliation: 5
- name: Qi Wang
equal-contrib: 3
affiliation: 3
- name: Marco Beccuti
equal-contrib: 4
affiliation: 2
- name: Raffaele Adolfo Calogero
equal-contrib: 4
affiliation: 4
- name: Luca Alessandri
equal-contrib: 5
affiliation: "3,4"
- name: Author with no affiliation
corresponding: true
affiliation: 3
affiliations:
- name: Politechnic of Turin, Torino, Italy
index: 1
- name: Department of Computer Science, University of Torino, Torino
index: 2
- name: Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
index: 3
- name: Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino
index: 4
- name: Molecular Biotechnology Center & Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
index: 5
date: 11 July 2022
bibliography: paper.bib
aas-doi:
aas-journal: JOSS The Journal of Open Source Software
---
Is this enough to load the citations? Here is my bib file.
#inproceedings{uno,
title={Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines},
author={N. Kulkarni , L. Alessandri, R. Panero, M. Arigoni, M. Olivero, G. Ferrero, et al},
booktitle={BMC Bioinformatic},
pages={vol. 19 Suppl 10:349, 2018, doi:10.1186/s12859-018-2296-x},
doi={10.1186/s12859-018-2296-x}
}
#inproceedings{due,
title={https://docs.docker.com/engine/}
}
#inproceedings{tre,
title={Containers in Bioinformatics: Applications, Practical Considerations, and Best Practices in Molecular Pathology},
author={S. Kadri, A. Sboner, A. Sigaras and S. Roy},
booktitle={J Mol Diagn., 2022},
doi={10.1016/j.jmoldx.2022.01.006}
}
#inproceedings{quattro,
title={https://cran.r-project.org/}
}
#inproceedings{cinque,
title={https://www.python.org/}
}
#inproceedings{sei,
title={Using R and Bioconductor in Clinical Genomics and Transcriptomics},
author={J.L. Sepulveda. },
booktitle={J Mol Diagn vol. 22},
doi={10.1016/j.jmoldx.2019.08.006}
}
#inproceedings{sette,
title={Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining},
author={L. Alessandri, F. Cordero, M. Beccuti, N. Licheri, M. Arigoni, M. Olivero, et al },
booktitle={NPJ Syst Biol Appl. vol. 7},
doi={10.1038/s41540-020-00162-6}
}
#inproceedings{otto,
title={Sparsely Connected Autoencoders: A Multi-Purpose Tool for Single Cell omics Analysis},
author={L. Alessandri, M.L. Ratto, S.G. Contaldo, M. Beccuti, F. Cordero, M. Arigoni, et al},
booktitle={nt J Mol Sci., vol. 22},
doi={10.3390/ijms222312755}
}
#inproceedings{nove,
title={rCASC: reproducible classification analysis of single-cell sequencing data},
author={L. Alessandri, F. Cordero, M. Beccuti, M. Arigoni, M. Olivero, G. Romano, et al},
booktitle={Gigascience, vol. 8},
doi={10.1093/gigascience/giz105}
}
#inproceedings{dieci,
title={https://docs.conda.io/en/latest/}
}
#inproceedings{undici,
title={https://bioconda.github.io/}
}
#inproceedings{dodici,
title={Orchestrating high-throughput genomic analysis with Bioconductor},
author={W. Huber, V.J. Carey, R. Gentleman, S. Anders, M. Carlson, B.S. Carvalho, et al},
booktitle={Nat Methods, vol. 12},
doi={10.1038/nmeth.3252}
}
#inproceedings{tredici,
title={Bioconductor: open software development for computational biology and bioinformatics},
author={R.C. Gentleman, V.J. Carey, D.M. Bates, B. Bolstad, M. Dettling, S. Dudoit, et al},
booktitle={Genome Biol., vol. 5},
doi={10.1186/gb-2004-5-10-r80}
}
#inproceedings{quattordici,
title={https://github.com/}
}
#inproceedings{quindici,
title={https://uwekorn.com/2021/03/01/deploying-conda-environments-in-docker-how-to-do-it-right.html}
}
#inproceedings{sedici,
title={https://pythonspeed.com/articles/activate-conda-dockerfile/}
}
#inproceedings{diciassette,
title={https://biocontainers.pro/}
}
In the text, how can i cite the first paper? I tried \cite{uno} as suggested from other questions but is not working. Here is the link to the repository https://github.com/alessandriLuca/CREDO_paper

Answer 1

In general, in pandoc's markdown, which JOSS uses, you can cite by doing [#bibtex-key], eg. in your first case, [#uno]. Here is the documentation regarding citations with pandoc's markdown.
The complete setup is demonstrated in the JOSS documentation: "Example paper and Bibliography".
Another way to see examples would be to look at how other papers on JOSS do it: see this paper which is the first one I find on JOSS. You can see there the [#bibtex-key] syntax.