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Cite in github readme Markdown

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

Solution

  • 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.