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# EMC Viroscience Website
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This repository contains the Quarto source code for the EMC Viroscience website, hosted at [https://lucvzon.github.io/EMC-Viroscience.github.io/](https://lucvzon.github.io/EMC-Viroscience.github.io/). The site serves as a central hub for bioinformatics workflow manuals, tool documentation, blog posts, and relevant links for the group.
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This repository contains the Quarto source code for the EMC Viroscience website, hosted at [https://EMC-Viroscience.github.io/](https://EMC-Viroscience.github.io/). The site serves as a central hub for bioinformatics workflow manuals, tool documentation, blog posts, and relevant links for the group.
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[](https://github.com/LucvZon/EMC-Viroscience.github.io/actions/workflows/deploy.yml)
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[](https://github.com/EMC-Viroscience/EMC-Viroscience.github.io/actions/workflows/deploy.yml)
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## Technology
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To preview the website locally before contributing:
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1. Ensure you have [Quarto installed](https://quarto.org/docs/get-started/).
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2. Clone this repository: `git clone https://github.com/LucvZon/EMC-Viroscience.github.io`
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2. Clone this repository: `git clone https://github.com/EMC-Viroscience/EMC-Viroscience.github.io`
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3. Navigate to the directory: `cd EMC-Viroscience.github.io`
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4. Run: `quarto preview`
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5. This will render the site locally and open it in your default web browser.
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We welcome contributions! Please see the detailed guide on the website:
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***[How to Contribute Manuals and Content](https://lucvzon.github.io/EMC-Viroscience.github.io/contribute/add_manuals.html)**
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***[How to Contribute Manuals and Content](https://EMC-Viroscience.github.io/contribute/add_manuals.html)**
Copy file name to clipboardExpand all lines: contribute/add_manuals.qmd
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We use the standard GitHub Fork & Pull Request workflow for contributions.
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1.**Fork the Repository:** Go to the main website repository: [https://github.com/LucvZon/EMC-Viroscience.github.io](https://github.com/LucvZon/EMC-Viroscience.github.io) and click the "Fork" button in the top-right corner. This creates a copy of the repository under your own GitHub account.
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1.**Fork the Repository:** Go to the main website repository: [https://github.com/EMC-Viroscience/EMC-Viroscience.github.io](https://github.com/EMC-Viroscience/EMC-Viroscience.github.io) and click the "Fork" button in the top-right corner. This creates a copy of the repository under your own GitHub account.
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2.**Clone Your Fork:** Clone the forked repository to your local machine:
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The maintainers of the EMC Viroscience website will review your pull request. They may ask for changes or clarifications. Once approved and merged, an automated process will render the site and deploy the changes.
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Thank you for contributing! If you have questions during this process, please feel free to open an issue on the [website repository's issue tracker](https://github.com/LucvZon/EMC-Viroscience.github.io/issues).
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Thank you for contributing! If you have questions during this process, please feel free to open an issue on the [website repository's issue tracker](https://github.com/EMC-Viroscience/EMC-Viroscience.github.io/issues).
Or go to the [github page](https://github.com/LucvZon/illumina-metagenomic-analysis-manual/releases/latest){target="_blank"} and manually download it there, then transfer it to your HPC system.
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Or go to the [github page](https://github.com/EMC-Viroscience/illumina-metagenomic-analysis-manual/releases/latest){target="_blank"} and manually download it there, then transfer it to your HPC system.
`singularity shell imam_workflow.sif` will drop you into a shell running inside the container. The conda environment needed for this workflow is automatically active on start-up of the interactive shell. All the tools of the conda environment will therefore be ready to use.
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Please note that you do not have to run `conda activate {environment}` to activate the environment – everything is inside imam_workflow.sif. If you're curious about the conda environment we're using, you can check it out [here](https://github.com/LucvZon/illumina-metagenomic-analysis-manual/blob/main/envs/environment.yml){target="_blank"}
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Please note that you do not have to run `conda activate {environment}` to activate the environment – everything is inside imam_workflow.sif. If you're curious about the conda environment we're using, you can check it out [here](https://github.com/EMC-Viroscience/illumina-metagenomic-analysis-manual/blob/main/envs/environment.yml){target="_blank"}
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## 1.4 Project Setup
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-p {project.folder} \
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-n {name} \
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-r {reads} \
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--ref-genome {reference} \
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--diamond-db {database} \
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-t {threads}
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```
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-`{name}`: The name of your study, no spaces allowed.
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-`{project.folder}`: The project folder where you run your workflow and store results.
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-`{reads}`: The folder that contains your raw .fastq.gz files. Raw read files must adhere to the naming scheme as described [here](https://help.basespace.illumina.com/files-used-by-basespace/fastq-files#naming){target="_blank"}.
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-`{reference}`: Absolute path pointing to your reference genome (.fna, .fasta, .fa).
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-`{database}`: Absolute path pointing to your diamond database (.dmnd).
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::: callout-important
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**The `--bind` arguments are needed to explicitly tell Singularity to mount the necessary host directories into the container.** The part before the colon is the path on the host machine that you want to make available. The path after the colon is the path inside the container where the host directory should be mounted.
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As a default, Singularity often automatically binds your home directory (`$HOME`) and the current directory (`$PWD`). We also explicitly bind `/mnt/viro0002-data` in this example. If your input files (reads, reference, databases) or output project directory reside outside these locations, you MUST add specific `--bind /host/path:/container/path` options for those locations, otherwise the container won’t be able to find them.
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:::
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::: callout-note
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When **prepare_project.py** prompts for the **reference genome** and **diamond database** paths, you must enter the absolute host paths, and these paths must be accessible via one of the bind mounts.
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Also, it'll ask if you want to create a raw_data/ folder with softlinks to your raw fastq.gz files. This is not required for running the workflow, but it can be convenient to have softlinks to your raw data available in your project directory.
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:::
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After running the prepare_project.py helper script, you should have the following files in your project directory:
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- The **sample.tsv** should have 3 columns: sample (sample name), fq1 and fq2 (paths to raw read files). Please note that samples sequenced by Illumina machines can be ran across different lanes. In such cases, the Illumina software will generate multiple fastq files for each sample that are lane specific (e.g. L001 = Lane 1, etc). So you may end up with a sample.tsv file that contains samples like `1_S1_L001` and `1_S1_L002`, even though these are the same sample, just sequenced across different lanes. The snakemake workflow will recognize this behaviour and merge these files together accordingly.
Or go to the [github page](https://github.com/LucvZon/nanopore-amplicon-analysis-manual/releases/latest){target="_blank"} and manually download it there, then transfer it to your HPC system.
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Or go to the [github page](https://github.com/EMC-Viroscience/nanopore-amplicon-analysis-manual/releases/latest){target="_blank"} and manually download it there, then transfer it to your HPC system.
`singularity shell naam_workflow.sif` will drop you into a shell running inside the container. The conda environment needed for this workflow is automatically active on start-up of the interactive shell. All the tools of the conda environment will therefore be ready to use.
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Please note that you do not have to run `conda activate {environment}` to activate the environment – everything is inside naam_workflow.sif. If you're curious about the conda environment we're using, you can check it out [here](https://github.com/LucvZon/nanopore-amplicon-analysis-manual/blob/main/envs/environment.yml){target="_blank"}
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Please note that you do not have to run `conda activate {environment}` to activate the environment – everything is inside naam_workflow.sif. If you're curious about the conda environment we're using, you can check it out [here](https://github.com/EMC-Viroscience/nanopore-amplicon-analysis-manual/blob/main/envs/environment.yml){target="_blank"}
If your Nextclade dataset contained a GFF3 annotation file for the reference sequence, then you can use the [viz_nextclade_cli.R](https://github.com/LucvZon/nanopore-amplicon-analysis-manual/tree/main/scripts) script to visualize the amino acid mutations per genetic feature. The plots will be generated for each genetic feature of the reference sequence and are output as plotly and ggplotly versions.
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If your Nextclade dataset contained a GFF3 annotation file for the reference sequence, then you can use the [viz_nextclade_cli.R](https://github.com/EMC-Viroscience/nanopore-amplicon-analysis-manual/tree/main/scripts) script to visualize the amino acid mutations per genetic feature. The plots will be generated for each genetic feature of the reference sequence and are output as plotly and ggplotly versions.
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Execute the following:
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```bash
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pangolin {input} --outfile {output}
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```
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-`{input}` is your aggregated consensus fasta file from step X.X.
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-`{input}` is your consensus fasta file from step 3.2.
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-`{output}` is a .csv file that contains taxon name and lineage assigned per fasta sequence. Read more about the output format: [https://cov-lineages.org/resources/pangolin/output.html](https://cov-lineages.org/resources/pangolin/output.html)
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