run prettier, fix tests to run with docker

.github/workflows/ci.yml

@@ -48,7 +48,7 @@ jobs:
         run: |
           wget -qO- https://get.nf-test.com | bash
           sudo mv nf-test /usr/local/bin/
-      
+
       - name: Run nf-test
         run: |
           nf-test test

CHANGELOG.md

@@ -6,4 +6,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## v0.1.0 - [Beta-Test-2024-11-29]
 
 ### `Added`
+
 - LegioVue pipeline created and initial beta code added

CITATIONS.md

@@ -8,42 +8,42 @@
 
 [Kraken2](https://github.com/DerrickWood/kraken2)
 
->Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
+> Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
 
 [Bracken](https://github.com/jenniferlu717/Bracken)
 
->Lu, J., Breitwieser, F. P., Thielen, P., and Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104. doi: 10.7717/peerj-cs.104
+> Lu, J., Breitwieser, F. P., Thielen, P., and Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104. doi: 10.7717/peerj-cs.104
 
 [Trimmomatic](https://github.com/usadellab/Trimmomatic)
 
->Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. doi: 10.1093/bioinformatics/btu170
+> Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120. doi: 10.1093/bioinformatics/btu170
 
 [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
->Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
+> Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
 
 [SPAdes](https://github.com/ablab/spades)
 
->Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., and Korobeynikov, A. (2020). Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics 70, e102. doi: 10.1002/cpbi.102
+> Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., and Korobeynikov, A. (2020). Using SPAdes De Novo Assembler. Current Protocols in Bioinformatics 70, e102. doi: 10.1002/cpbi.102
 
 [QUAST](https://github.com/ablab/quast)
 
->Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich,
-WebQUAST: online evaluation of genome assemblies,
-Nucleic Acids Research (2023) 51 (W1): W601–W606. doi: 10.1093/nar/gkad406
+> Alla Mikheenko, Vladislav Saveliev, Pascal Hirsch, Alexey Gurevich,
+> WebQUAST: online evaluation of genome assemblies,
+> Nucleic Acids Research (2023) 51 (W1): W601–W606. doi: 10.1093/nar/gkad406
 
 [el_gato](https://github.com/appliedbinf/el_gato)
 
->Alan Collins, Dev Mashruwala, Andrew Conley, Lavanya Rishishwar, Emily T. Norris, Anna Gaines, Will Overholt. Epidemiology of Legionella : Genome-bAsed Typing. Available online at: https://github.com/appliedbinf/el_gato
+> Alan Collins, Dev Mashruwala, Andrew Conley, Lavanya Rishishwar, Emily T. Norris, Anna Gaines, Will Overholt. Epidemiology of Legionella : Genome-bAsed Typing. Available online at: https://github.com/appliedbinf/el_gato
 
 [chewBBACA](https://github.com/B-UMMI/chewBBACA)
 
->Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:000166. doi:10.1099/mgen.0.000166
+> Silva M, Machado MP, Silva DN, Rossi M, Moran-Gilad J, Santos S, Ramirez M, Carriço JA. 2018. chewBBACA: A complete suite for gene-by-gene schema creation and strain identification. Microb Genom 4:000166. doi:10.1099/mgen.0.000166
 
 [ReporTree](https://github.com/insapathogenomics/ReporTree)
 
->Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V (2023) ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Medicine. doi: 10.1186/s13073-023-01196-1
+> Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V (2023) ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Medicine. doi: 10.1186/s13073-023-01196-1
 
 [GrapeTree](https://github.com/achtman-lab/GrapeTree)
 
->Zhou, Z., Alikhan, N.-F., Sergeant, M. J., Luhmann, N., Vaz, C., Francisco, A. P., et al. (2018). GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 28, 1395–1404. doi: 10.1101/gr.232397.117
+> Zhou, Z., Alikhan, N.-F., Sergeant, M. J., Luhmann, N., Vaz, C., Francisco, A. P., et al. (2018). GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens. Genome Res. 28, 1395–1404. doi: 10.1101/gr.232397.117