From 5cef13caf1a2bc66800af8e228dd1041ad7fbe86 Mon Sep 17 00:00:00 2001 From: Sage Wright Date: Wed, 11 Sep 2024 14:59:02 +0000 Subject: [PATCH] organize the assets folder to a more intuitive structure --- .../Core_Gene_SNP.png | Bin .../Create_Terra_Table_example1.png} | Bin .../Create_Terra_Table_example2.png} | Bin .../Find_Shared_Variants_PHB.png | Bin .../{freyja => figures}/Freyja_FASTQ.png | Bin .../Freyja_figure2.png} | Bin .../Freyja_figure3.png} | Bin .../{standalone => figures}/Kraken2.png | Bin .../lyve_set.png => figures/Lyve_Set.png} | Bin .../Snippy_Streamline.png | Bin .../Snippy_Streamline_FASTA.png | Bin .../Snippy_Variants.png | Bin .../TheiaCoV.png | Bin .../TheiaEuk_Illumina_PE.png | Bin .../TheiaMeta_Illumina_PE.png | Bin .../TheiaProk.png | Bin .../TheiaValidate.png | Bin .../{ => figures}/Workflow_Relationships.png | Bin .../Workflow_Relationships_dark.png | Bin .../{ => figures}/basespace_fetch/step1.png | Bin .../{ => figures}/basespace_fetch/step10.png | Bin 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a/docs/assets/Theiagen-Logo-White.png b/docs/assets/logos/Theiagen-Logo-White.png similarity index 100% rename from docs/assets/Theiagen-Logo-White.png rename to docs/assets/logos/Theiagen-Logo-White.png diff --git a/docs/assets/Theiagen-Symbol-Standard-01.png b/docs/assets/logos/Theiagen-Symbol-Standard-01.png similarity index 100% rename from docs/assets/Theiagen-Symbol-Standard-01.png rename to docs/assets/logos/Theiagen-Symbol-Standard-01.png diff --git a/docs/assets/new_workflow_template.md b/docs/assets/new_workflow_template.md index 1423b4a90..9e7ef6799 100644 --- a/docs/assets/new_workflow_template.md +++ b/docs/assets/new_workflow_template.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Workflow Type](../../workflows_overview/workflows-type.md/#link-to-workflow-type) | [Applicable Kingdom](../../workflows_overview/workflows-kingdom.md/#link-to-applicable-kingdom) | PHB | | | +| [Workflow Type](../../workflows_overview/workflows_type.md/#link-to-workflow-type) | [Applicable Kingdom](../../workflows_overview/workflows_kingdom.md/#link-to-applicable-kingdom) | PHB | | | ## Workflow_Name_On_Terra diff --git a/docs/code_contribution.md b/docs/contributing/code_contribution.md similarity index 100% rename from docs/code_contribution.md rename to docs/contributing/code_contribution.md diff --git a/docs/contribution_guide.md b/docs/contributing/doc_contribution.md similarity index 87% rename from docs/contribution_guide.md rename to docs/contributing/doc_contribution.md index 45b021b02..8a32abf56 100644 --- a/docs/contribution_guide.md +++ b/docs/contributing/doc_contribution.md @@ -40,29 +40,22 @@ Here are some VSCode Extensions can help you write and edit your markdown files A brief description of the documentation structure is as follows: - `docs/` - Contains the Markdown files for the documentation. - - `index.md` - The home page for the PHB documentation. - - `contributing_guide.md` - This file. - `assets/` - Contains images and other files used in the documentation. - - `basespace_fetch/` - Contains images for the BaseSpace_Fetch workflow. - - `characterization/` - Contains workflow diagrams for the characterization workflows AND the template QC check tables for those workflows. - - `create_terra_table/` - Contains images for the Create_Terra_Table workflow. - - `freyja/` - Contains images for the Freyja workflow. + - `figures/` - Contains images, figures, and workflow diagrams used in the documentation. For workflows that contain many images (such as BaseSpace_Fetch), it is recommended to create a subdirectory for the workflow. + - `files/` - Contains files that are used in the documentation. This may include example outputs or templates. For workflows that contain many files (such as TheiaValidate), it is recommended to create a subdirectory for the workflow. + - `logos/` - Contains Theiagen logos and symbols used int he documentation. - `metadata_formatters/` - Contains the most up-to-date metadata formatters for our submission workflows. - - `misc_files/` - Contains example outputs and various other files used in the documentation. - - `phylo_diagrams/` - Contains images for the phylogenetic workflows. - - `standalone/` - Contains images for the standalone workflows. - - `theiavalidate/` - Contains example input and outputs for the TheiaValidate workflow. - - `new_workflow_template.md` - A template for new workflow pages. - - `Theiagen-Logo-White.png` - The Theiagen logo in white - - `Theiagen-Symbol-Standard-01.png` - The Theiagen symbol in standard colors - - `Workflow_Relationships_dark.png` - A diagram showing the relationships between the various workflows suitable for dark mode - - `Workflow_Relationships.png` - A diagram showing the relationships between the various workflows suitable for light mode + - `new_workflow_template.md` - A template for adding a new workflow page to the documentation. + - `contributing/` - Contains the Markdown files for our contribution guides, such as this file - `javascripts/` - Contains JavaScript files used in the documentation. - `tablesort.js` - A JavaScript file used to enable table sorting in the documentation. + - `overrides/` - Contains HTMLs used to override theme defaults + - `main.html` - Contains the HTML used to display a warning when the latest version is not selected - `stylesheets/` - Contains CSS files used in the documentation. - `extra.css` - A custom CSS file used to style the documentation; contains all custom theme elements (scrollable tables, resizable columns, Theiagen colors), and custom admonitions. - `workflows/` - Contains the Markdown files for each workflow, organized into subdirectories by workflow category - `workflows_overview/` - Contains the Markdown files for the overview tables for each display type: alphabetically, by applicable kingdom, and by workflow type. + - `index.md` - The home/landing page for our documentation. ### Adding a Page for a New Workflow {#new-page} @@ -79,9 +72,9 @@ If you are adding a new workflow, there are a number of things to do in order to - Link to the workflow on Dockstore (if applicable) - Workflow name linked to the information tab on Dockstore. 3. Format this information in a table. 4. Copy the previously gathered information to ==**ALL THREE**== overview tables in `docs/workflows_overview/`: - - `workflows-alphabetically.md` - Add the workflow in the appropriate spot based on the workflow name. - - `workflows-kingdom.md` - Add the workflow in the appropriate spot(s) based on the kingdom(s) the workflow is applicable to. Make sure it is added alphabetically within the appropriate subsection(s). - - `workflows-type.md` - Add the workflow in the appropriate spot based on the workflow type. Make sure it is added alphabetically within the appropriate subsection. + - `workflows_alphabetically.md` - Add the workflow in the appropriate spot based on the workflow name. + - `workflows_kingdom.md` - Add the workflow in the appropriate spot(s) based on the kingdom(s) the workflow is applicable to. Make sure it is added alphabetically within the appropriate subsection(s). + - `workflows_type.md` - Add the workflow in the appropriate spot based on the workflow type. Make sure it is added alphabetically within the appropriate subsection. 5. Copy the path to the workflow to ==**ALL**== of the appropriate locations in the `mkdocs.yml` file (under the `nav:` section) in the main directory of this repository. These should be the exact same spots as in the overview tables but without additional information. This ensures the workflow can be accessed from the navigation sidebar. ## Standard Language & Formatting Conventions diff --git a/docs/getting_started/commandline.md b/docs/getting_started/commandline.md new file mode 100644 index 000000000..b5a1dc7b6 --- /dev/null +++ b/docs/getting_started/commandline.md @@ -0,0 +1,352 @@ + + +## Step 1: Obtain the Workflow and Data + +You will need to have access to the WDL workflow file (.wdl) and any associated input files (such as reference genomes, input data files, etc.). To do this, complete the following steps: + +### **1. Install Git (if not already installed)** + +If you don't already have Git installed on your system, you will need to install it. Here's how you can install Git on some common operating systems: + +- **Linux (Ubuntu/Debian)** + + ```bash + sudo apt update + sudo apt install git + ``` + +- **macOS** + + Git is usually pre-installed on macOS. However, you can install or update it using Homebrew: + + ```bash + brew install git + ``` + +- **Windows** + + Download and install Git from the official website: https://git-scm.com/download/win + + +### 2. Clone the Repository + +1. Open your terminal. +2. Create a directory where you want to store the cloned repository and navigate to it. + + ```bash + mkdir /path/to/your/desired/new/directory + cd /path/to/your/desired/new/directory + ``` + +3. Clone the https://github.com/theiagen/public_health_bioinformatics repository from GitHub using the following command: + + ```bash + git clone https://github.com/theiagen/public_health_bioinformatics.git + ``` + +4. After running the command, Git will download all the repository files and set up a local copy in the directory you specified. + +### 3. Navigate to the Cloned Repository + +1. Change your working directory to the newly cloned repository: + + ```bash + cd public_health_bioinformatics + ``` + +2. You're now inside the cloned repository's directory. Here, you should find all the files and directories from the GitHub repository. + +### 4. Verify the Cloned Repository + +You can verify that the repository has been cloned successfully by listing the contents of the current directory using the `ls` (on Linux/macOS) or `dir` (on Windows) command: + +```bash +ls +``` + +This should display the files and directories within the https://github.com/theiagen/public_health_bioinformatics.git repository. + +Congratulations! You've successfully cloned the https://github.com/theiagen/public_health_bioinformatics.git repository from GitHub to your local command line environment. You're now ready to proceed with running the bioinformatics analysis workflows using WDL as described in subsequent steps. + +## Step 2: Install docker and miniWDL + +Docker and miniwdl will be required for command line execution. We will check if these are installed on your system and if not, install them now. + +[Docker](https://www.notion.so/Docker-771022d648f946a1aff949d14dc79f54?pvs=21) + +[miniwdl](https://www.notion.so/miniwdl-019e697fee6d4216bdb543754e6efe49?pvs=21) + +1. Open your terminal. +2. Navigate to the directory where your workflow and input files are located using the `cd` command: + + ```bash + cd /path/to/your/workflow/directory + ``` + +3. Check if Docker is installed: + + ```bash + docker --version + ``` + + If Docker is not installed, follow the official installation guide for your operating system: [**https://docs.docker.com/get-docker/**](https://docs.docker.com/get-docker/) + +4. Check if **`miniwdl`** is installed: + + ```bash + miniwdl --version + ``` + + If **`miniwdl`** is not installed, you can install it using pip: + + ```bash + pip install miniwdl + ``` + + +## Step 3: Set up the input.json file for your WDL workflow + +In a WDL (Workflow Description Language) workflow, an input JSON file is used to provide attributes (values/files etc) for input variables into the workflow. The names of the input variables must match the names of inputs specified in the workflow file. The workflow files can be found within the git repository that you cloned. Each input variable can have a specific type of attribute, such as String, File, Int, Boolean, Array, etc. Here's a detailed outline of how to specify different types of input variables in an input JSON file: + +- **String Input** + + To specify a string input, use the name of the input variable as the key and provide the corresponding string value. Example: + + ```json + { + "sampleName": "VirusSample1", + "primerSequence": "ACGTGTCAG" + } + ``` + +- **File Input** + + To specify a file input, provide the path to the input file relative to the directory where you run the `miniwdl` command. Example: + + ```json + { + "inputFastq": "data/sample.fastq", + "referenceGenome": "reference/genome.fasta" + } + + ``` + +- **Int Input** + + To specify an integer input, provide the integer value. These do not require quotation marks. Example: + + ```json + { + "minReadLength": 50, + "maxThreads": 8 + } + ``` + +- **Boolean Input** + + To specify a boolean input, use `true` or `false` (lowercase). Example: + + ```json + { + "useQualityFiltering": true, + "useDuplicateRemoval": false + } + ``` + +- **Array Input** + + To specify an array input, provide the values as an array. Example: + + ```json + { + "sampleList": ["Sample1", "Sample2", "Sample3"], + "thresholds": [0.1, 0.05, 0.01] + } + ``` + + +## Step 4: Execute the Workflow + +Run the workflow using `miniwdl` with the following command, replacing `your_workflow.wdl` with the actual filename of your WDL workflow and `input.json` with the filename of your input JSON file. + +```bash +miniwdl run your_workflow.wdl --input input.json +``` + +## Step 5: Monitor Workflow Progress + +You can monitor the progress of the workflow by checking the console output for updates and log messages. This can help you identify any potential issues or errors during execution. + +### Tips for monitoring your workflow + +After you've started the workflow using the **`miniwdl run`** command, you'll see various messages appearing in the terminal. These messages provide information about the various steps of the workflow as they are executed. Monitoring this output is crucial for ensuring that the workflow is progressing as expected. + +The console output will typically show: + +1. **Task Execution:** You will see messages related to the execution of individual tasks defined in your workflow. These messages will include details about the task's name, input values, and progress. +2. **Logging Information:** Workflow tasks often generate log messages to provide information about what they are doing. These logs might include details about software versions, input data, intermediate results, and more. +3. **Execution Progress:** The output will indicate which tasks have completed and which ones are currently running. This helps you track the overall progress of the workflow. +4. **Error Messages:** If there are any errors or issues during task execution, they will be displayed in the console output. These error messages can help you identify problems and troubleshoot them. +5. **Timing Information:** You might also see timing information for each task, indicating how long they took to execute. This can help you identify tasks that might be taking longer than expected. + +### **Example Console Output:** + +Here's an example of what the console output might look like while the workflow is running: + +```groovy + +Running: task1 +Running: task2 +Completed: task1 (Duration: 5s) +Running: task3 +Error: task2 (Exit Code: 1) +Running: task4 +... + +``` + +In this example, you can see that **`task1`** completed successfully in 5 seconds, but **`task2`** encountered an error and exited with a non-zero exit code. This kind of output provides insight into the progress and status of the workflow. + +### **What to Look For:** + +As you monitor the console output, pay attention to: + +- **Successful Task Completion:** Look for messages indicating tasks that have completed successfully. This ensures that the workflow is progressing as intended. +- **Error Messages:** Keep an eye out for any error messages or tasks that exit with non-zero exit codes. These indicate issues that need attention. +- **Task Order:** The order of task messages can provide insights into the workflow's logic and execution flow. +- **Timing:** Notice how long each task takes to complete. If a task takes significantly longer than expected, it might indicate a problem. + +### Early **Troubleshooting:** + +If you encounter errors or unexpected behavior, the console output can provide valuable information for troubleshooting. You can search for the specific error messages to understand the problem and take appropriate action, such as correcting input values, adjusting parameters, or addressing software dependencies. + +Monitoring the workflow progress through the console output is an essential practice for successful execution. It allows you to track the status of individual tasks, identify errors, and ensure that your analysis is proceeding as planned. Regularly reviewing the output will help you address any issues and improve the efficiency of your bioinformatics workflow. + +### What to do if you need to cancel a run + +Canceling a running workflow is an important step in case you need to stop the execution due to errors, unexpected behavior, or any other reason. If you're using `miniwdl` to run your workflow, here's how you can cancel a workflow run while it's in progress: + +1. **Ctrl + C**: The simplest way to cancel a running command in the terminal is to press `Ctrl + C`. This sends an interrupt signal to the running process, which should gracefully terminate it. However, keep in mind that this might not work for all scenarios, and some tasks might not be able to cleanly terminate. +2. **Terminate Docker Containers**: If your workflow involves Docker containers, you might need to ensure that any Docker containers launched by the workflow are also terminated. To do this, you can manually stop the Docker containers associated with the workflow. You can use the `docker ps` command to list running containers and `docker stop ` to stop a specific container. +3. **Kill the miniwdl Process**: If the `Ctrl + C` approach doesn't work, you might need to explicitly kill the `miniwdl` process running in the terminal. To do this, you can use the `kill` command. First, find the process ID (PID) of the `miniwdl` process by running: + + ```bash + ps aux | grep miniwdl + + ``` + + Identify the PID in the output and then run: + + ```bash + kill -9 + + ``` + + This forcefully terminates the process. + +4. **Clean Up Intermediate Files**: Depending on the workflow and how tasks are structured, there might be intermediate files or resources that were generated before the cancellation. You might need to manually clean up these files to free up disk space. +5. **Check for Workflow-Specific Cancellation**: Some workflows might have specific mechanisms to handle cancellation. Refer to the workflow documentation or user guide to understand if there's a recommended way to cancel the workflow gracefully. +6. **Check for Any Remaining Resources**: After canceling the workflow, it's a good practice to check for any remaining resources that might need to be cleaned up. This could include temporary files, Docker images, or other resources that were created during the workflow's execution. + +Remember that canceling a workflow might leave the system in an inconsistent state, especially if some tasks were partially executed. After canceling, it's a good idea to review the output and logs to identify any cleanup actions you might need to take. + +It's important to approach workflow cancellation carefully, as abruptly terminating processes can potentially lead to data loss or other unintended consequences. Always make sure you understand the workflow's behavior and any potential side effects of cancellation before proceeding. + +## Step 6: Review Output + +Once the workflow completes successfully, you will find the output files and results in the designated output directory as defined in your WDL workflow. + +- **Substep 1: Locate the Output Directory** + + Before you begin reviewing outputs, make sure you know where the output directory of your workflow is located. This is typically specified in the workflow configuration or input JSON file. Navigate to this directory using the **`cd`** command in your terminal. + + ```bash + cd /path/to/your/output/directory + ``` + +- **Substep 2: Logs** + + Logs are a valuable source of information about what happened during each step of the workflow. Each task in the workflow might generate its own log file. Here's how to review logs: + + 1. Use the **`ls`** command to list the files in the output directory: + + ```bash + + ls + + ``` + + 2. Look for log files with names that correspond to the tasks in your workflow. These files often have a **`.log`** extension. + 3. Open a log file using a text editor like **`less`** or **`cat`**: + + ```bash + + less task_name.log + + ``` + + Use the arrow keys to navigate through the log, and press **`q`** to exit. + + 4. Inspect the log for messages related to the task's execution, input values, software versions, and any errors or warnings that might have occurred. + +- **Substep 3: stderr (Standard Error) and stdout (Standard Output)** + + stderr and stdout are streams where processes write error messages and standard output, respectively. These are often redirected to files during workflow execution. Here's how to review them: + + 1. Use the **`ls`** command to list the files in the output directory. + 2. Look for files with names like **`task_name.err`** (for stderr) and **`task_name.out`** (for stdout). + 3. Open the files using a text editor: + + ```bash + + less task_name.err + less task_name.out + + ``` + + These files might contain additional information about the task's execution, errors, and output generated during the analysis. + +- **Substep 4: Reviewing Output Files** + + Workflow tasks might generate various types of output files, such as plots, reports, or data files. Here's how to review them: + + 1. Use the **`ls`** command to list the files in the output directory. + 2. Identify the files generated by your workflow tasks. + 3. Depending on the file type, you can use different tools to open and view them. For example, you might use **`less`** or a text editor for text-based files, or an image viewer for image files. +- **Substep 5: Interpretation and Troubleshooting** + + As you review the outputs, keep these points in mind: + + - **Successful Execution:** Look for indicators of successful task execution, such as expected messages, correct output files, and absence of error messages. + - **Errors and Warnings:** Pay close attention to any error or warning messages in logs, stderr, or stdout. These can help you identify issues that need troubleshooting. + - **Input Values and Parameters:** Verify that input values and parameters were correctly passed to tasks. Incorrect input can lead to unexpected behavior. + - **Software Versions:** Check if the versions of the tools and software used in the workflow match what you expected. + - **Intermediate Outputs:** Review intermediate outputs generated by tasks. These might provide insights into the workflow's progress and results. +- **Substep 6: Make Notes and Take Action** + + As you review the outputs, make notes of any issues, errors, or unexpected behavior you encounter. Depending on the severity of the issues, you might need to: + + - Adjust input parameters. + - Re-run specific tasks. + - Debug and troubleshoot errors. + - Consult the workflow documentation. + - Reach out to the Theiagen Genomics bioinformatics experts for assistance. (support@terrapublichealth.zendesk.com) + +**Conclusion** + +Reviewing the outputs of your bioinformatics workflow is a critical step to ensure the quality of your analysis. Logs, stderr, stdout, and generated output files provide valuable insights into the execution process and results. By carefully reviewing these outputs and addressing any issues, you can enhance the reliability and accuracy of your bioinformatics analysis. + +## Step 7: Troubleshooting and Debugging + +1. If the workflow encounters errors or fails to execute properly, review the error messages in the terminal. +2. Check for any missing input files, incorrect paths, or issues related to software dependencies. +3. Double-check your input JSON file to ensure that all required inputs are correctly specified. + +Congratulations! You have successfully executed a bioinformatics analysis workflow using WDL on the command line. This tutorial covered the basic steps to run a WDL workflow using the `miniwdl` command line tool. + +Remember that the specific steps and commands might vary depending on the details of your workflow, software versions, and environment. Be sure to consult the documentation for `miniwdl`, WDL, and any other tools you're using for more advanced usage and troubleshooting. + +Happy analyzing! \ No newline at end of file diff --git a/docs/getting_started/terra.md b/docs/getting_started/terra.md new file mode 100644 index 000000000..0df933c24 --- /dev/null +++ b/docs/getting_started/terra.md @@ -0,0 +1,114 @@ +# Getting Started with Genomic Analysis in Public Health + + + + + + + +![**Analysis Approaches for Genomic Data:** This diagram shows the Theiagen workflows (green boxes) available on Terra for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. Descriptions of these functions and their workflows can be found in the [Getting Started with Genomic Analysis in Public Health](https://www.notion.so/PHB-main-DO-NOT-EDIT-7ffec467deea4bcca85576040cad6262?pvs=21) section below. The yellow boxes show functions that may be undertaken independently of workflows on Terra.](https://prod-files-secure.s3.us-west-2.amazonaws.com/be290196-9090-4f3c-a9ab-fe730ad213e0/d16a913d-2aa6-46af-a3f7-fd14390b47f0/Workflow__Relationships_(4)_(1).png) + +**Analysis Approaches for Genomic Data:** This diagram shows the Theiagen workflows (green boxes) available on Terra for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. Descriptions of these functions and their workflows can be found in the [Getting Started with Genomic Analysis in Public Health](https://www.notion.so/PHB-main-DO-NOT-EDIT-7ffec467deea4bcca85576040cad6262?pvs=21) section below. The yellow boxes show functions that may be undertaken independently of workflows on Terra. + +# Data Import to Terra + +To start using Terra for data analysis, you will first need to import your data into your workspace. There are multiple ways to do this: + +- **Using Terra’s native features to upload data from your local computer or link to data that’s already in a Google bucket** +- Data import workflows + - Using the [SRA_Fetch](https://www.notion.so/SRA_Fetch-46bef1c62593438b9a6c8b9256442fa1?pvs=21) workflow to import publicly available data from any repository in the [INSDC](https://www.insdc.org/) (including with [SRA](https://www.ncbi.nlm.nih.gov/sra), [ENA](https://www.ebi.ac.uk/ena/browser/home) and [DRA](https://www.ddbj.nig.ac.jp/dra/index-e.html)) + - Using the [Assembly_Fetch ](https://www.notion.so/Assembly_Fetch-fe838a9ada184166975c6ff7c143e99b?pvs=21) workflow to import publicly available genome assemblies from [NCBI](https://www.ncbi.nlm.nih.gov/datasets/) + - Using the [BaseSpace_Fetch](https://www.notion.so/BaseSpace_Fetch-ebece1219552422cb143cb316ad59b5b?pvs=21) workflow to import data from your [Illumina BaseSpace](https://basespace.illumina.com/) account + + + + +# Genome assembly, QC, and characterization + +## Theia workflows + +The Theia workflows are used for genome assembly, quality control, and characterization. The [TheiaCoV Workflow Series](https://www.notion.so/TheiaCoV-Workflow-Series-47e3269a932343be982507d72fcb0fbe?pvs=21), [TheiaProk Workflow Series](https://www.notion.so/TheiaProk-Workflow-Series-6ae7afc7b3544b889fda7c758ea436e1?pvs=21), and [TheiaEuk Workflow Series](https://www.notion.so/TheiaEuk-Workflow-Series-516a773fb418424c876792ea8dba3fde?pvs=21) workflows are intended for viral, bacterial, and fungal pathogens, respectively. [TheiaMeta Workflow Series](https://www.notion.so/TheiaMeta-Workflow-Series-a9a9d5d52e02474189c1d7b3225f3ffe?pvs=21) is intended for the analysis of a single taxon from metagenomic data. + + + +## Quality evaluation + +The TheiaX workflows will generate various quality metrics. These should be evaluated relative to quality thresholds that have been agreed upon within your laboratory or sequencing program and define the sufficient quality characteristics for a genome and sequence data to be used. For the [TheiaCoV Workflow Series](https://www.notion.so/TheiaCoV-Workflow-Series-47e3269a932343be982507d72fcb0fbe?pvs=21), [TheiaProk Workflow Series](https://www.notion.so/TheiaProk-Workflow-Series-6ae7afc7b3544b889fda7c758ea436e1?pvs=21), and [TheiaEuk Workflow Series](https://www.notion.so/TheiaEuk-Workflow-Series-516a773fb418424c876792ea8dba3fde?pvs=21) workflows, this quality evaluation may be undertaken using the optional `QC_check` task. Full instructions for the use of this task may be found on the relevant workflow page. Some quality metrics are not evaluated by the `QC_check` task and should be evaluated manually. + +Genomes that fail to meet agreed quality thresholds should not be used. Results for characterization of these genomes may be inaccurate or unreliable. The inclusion of poor-quality genomes in downstream comparative analyses will bias their results. Samples that fail to meet QC thresholds will need to be re-sequenced and sample processing may need to be repeated (e.g. culture-based isolation of clonal bacteria, DNA/RNA extraction, and processing for sequencing). + +## Update workflows for SARS-CoV-2 genomes + +Workflows are available for updating the Pangolin and VADR assignments made to SARS-CoV-2 genomes. The [Pangolin Update](https://www.notion.so/Pangolin-Update-4763e30105f343a5ab6a1a1dd315a976?pvs=21) workflow accounts for the delay in assigning names to newly emerging lineages that you may have already sequenced. The [VADR_Update](https://www.notion.so/VADR_Update-a6398bceef7f408b8b3a7334a2b243c5?pvs=21) workflow similarly accounts for features that have been newly identified in SARS-CoV-2 genomes when assessing genome quality with VADR. + +# Phylogenetics + +## Phylogenetic construction + +Phylogenetic trees are constructed to assess the evolutionary relationships between sequences in the tree. These evolutionary relationships are often used as a proxy for epidemiological relationships, and sometimes for inferring transmission between isolation sources. + +There are various methods for constructing phylogenetic trees, depending on the sequencing data being used, the organism being analyzed and how it evolved, what you would like to infer from the tree, and the computational resources available for the tree construction. Theiagen has a number of workflows for constructing phylogenetic trees. For full details of these workflows, please see [Guide to Phylogenetics](https://www.notion.so/Guide-to-Phylogenetics-c997fe59e3f0423aa8a73eeccccd1b92?pvs=21) which includes advice on the appropriate tree-building workflows and phylogenetic visualization approaches. + + + +## Phylogenetic placement + +Phylogenetic placement is used to place your own sequences onto an existing phylogenetic tree. This may be used to find the closest relatives to your sequence(s). More details, including phylogenetic visualization approaches can be found in [Guide to Phylogenetics](https://www.notion.so/Guide-to-Phylogenetics-c997fe59e3f0423aa8a73eeccccd1b92?pvs=21) + +# Public Data Sharing + + + +# **SARS-CoV-2 Metagenomic Analysis** + + \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index f9c144efd..14bfe3f4f 100644 --- a/docs/index.md +++ b/docs/index.md @@ -14,8 +14,8 @@ Theiagen's approach to genomic analysis in public health typically uses the [Ter **When undertaking genomic analysis using Terra and other data visualization platforms, it is essential to consider the necessary and appropriate workflows and resources for your analysis. To help you make these choices, take a look at the relationship between the most commonly used Theiagen workflows.** !!! caption "Analysis Approaches for Genomic Data" - ![The relationship between the various PHB workflows](assets/Workflow_Relationships.png#only-light){data-description="This diagram shows the Theiagen workflows (green boxes) available for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. The yellow boxes show functions that may be undertaken independently of workflows on Terra."} - ![The relationship between the various PHB workflows](assets/Workflow_Relationships_dark.png#only-dark){data-description="This diagram shows the Theiagen workflows (green boxes) available for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. The yellow boxes show functions that may be undertaken independently of workflows on Terra."} + ![The relationship between the various PHB workflows](assets/figures/Workflow_Relationships.png#only-light){data-description="This diagram shows the Theiagen workflows (green boxes) available for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. The yellow boxes show functions that may be undertaken independently of workflows on Terra."} + ![The relationship between the various PHB workflows](assets/figures/Workflow_Relationships_dark.png#only-dark){data-description="This diagram shows the Theiagen workflows (green boxes) available for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. The yellow boxes show functions that may be undertaken independently of workflows on Terra."} This diagram shows the Theiagen workflows (green boxes) available for analysis of genomic data in public health and the workflows that may be used consecutively (arrows). The blue boxes describe the major functions that these workflows undertake. The yellow boxes show functions that may be undertaken independently of workflows on Terra. @@ -37,3 +37,70 @@ If you would like to submit suggested code changes to our workflows, you may add ### About Theiagen Theiagen develops bioinformatics solutions for public health labs, and then trains and supports scientists to use these. If you would like to work with Theiagen, please [get in contact](https://theiagen.com/team-up-with-theiagen/). + +------ + +The PHB repository contains workflows for the characterization, genomic epidemiology, and sharing of pathogen genomes of public health concern. Workflows are available for viruses, bacteria, and fungi. + +All workflows in the PHB repository end with _PHB in order to differentiate them from earlier versions and from the original tools they incorporate. + +Briefly, the main genomic characterization workflows are split by pathogen type: + +Viral (TheiaCoV workflows) +Bacterial (TheiaProk workflows) +Fungal (TheiaEuk workflows) +Many more workflows are available, and are documented in detail in the Theiagen Public Resources Documentation. + +On the Shoulder of Giants +The PHB repository would not be possible without its predecessors. We would like to acknowledge the following repositories, individuals, and contributors for their influence on the development of these workflows: + +The PHB repository originated from collaborative work with Andrew Lang, PhD & his Genomic Analysis WDL workflows. The workflows and task development were influenced by The Broad's Viral Pipes repository. The TheiaCoV workflows for viral genomic characterization were influenced by UPHL's Cecret & StaPH-B's Monroe workflows. The TheiaProk workflows for bacterial genomic characterization were influenced by Robert Petit's bactopia. Most importantly, the PHB user community drove the development of these workflows and we are grateful for their feedback and contributions. + +If you would like to provide feedback, please raise a GitHub issue. + +Contributing to the PHB workflows +We warmly welcome contributions to this repository! Our style guide may be found here for convenience of formatting. + +You can expect a careful review of every PR and feedback as needed before merging, just like we do for PRs submitted by the Theiagen team. Our PR template can help prepare you for the review process. As always, reach out with any questions! We love recieving feedback and contributions from the community. When your PR is merged, we'll add your name to the contributors list below! + +Authorship & Responsibility +Authorship +(Ordered by contribution [# of lines changed] as of 2024-08-01) + +Sage Wright (@sage-wright) - Conceptualization, Software, Validation, Supervision +Inês Mendes (@cimendes) - Software, Validation +Curtis Kapsak (@kapsakcj) - Conceptualization, Software, Validation +James Otieno (@jrotieno) - Software, Validation +Frank Ambrosio (@frankambrosio3) - Conceptualization, Software, Validation +Michelle Scribner (@michellescribner) - Software, Validation +Kevin Libuit (@kevinlibuit) - Conceptualization, Project Administration, Software, Validation, Supervision +Emma Doughty (@emmadoughty) - Software, Validation +Andrew Page (@andrewjpage) - Project Administration, Software, Supervision +Andrew Lang (@AndrewLangVt) - Software, Supervision +Kelsey Kropp (@kelseykropp) - Validation +Emily Smith (@emily-smith1) - Validation +Joel Sevinsky (@sevinsky) - Conceptualization, Project Administration, Supervision +External Contributors +We would like to gratefully acknowledge the following individuals from the public health community for their contributions to the PHB repository: + +Robert Petit (@rpetit3) +Ash O'Farrel (@aofarrel) +Sam Baird (@sam-baird) +Holly Halstead (@HNHalstead) +Maintaining PHB Pipelines +Theiagen Genomics has committed to maintaining these workflows for the forseeable future. These workflows are written using a standard workflow language (WDL) and uses Docker images based on the StaPHB-B Docker Builds. New versions that include bug fixes and additional features are released on a quarterly bases, with urgent bug fixes released as needed. Each version is accompanied by detailed release notes to lower the barrier of pipeline upkeep from the public health community at large. + +Point of Contact +If you have any questions or concerns, please raise a GitHub issue or email Theiagen's general support at support@theiagen.com. + +Conflict of Interest +The authors declare no conflict of interest. + +Citation +Please cite this paper if publishing work using any workflows: + +Libuit, Kevin G., Emma L. Doughty, James R. Otieno, Frank Ambrosio, Curtis J. Kapsak, Emily A. Smith, Sage M. Wright, et al. 2023. “Accelerating Bioinformatics Implementation in Public Health.” Microbial Genomics 9 (7). https://doi.org/10.1099/mgen.0.001051. + +Alternatively, please cite this paper if using the TheiaEuk workflow: + +Ambrosio, Frank, Michelle Scribner, Sage Wright, James Otieno, Emma Doughty, Andrew Gorzalski, Danielle Siao, et al. 2023. “TheiaEuk: A Species-Agnostic Bioinformatics Workflow for Fungal Genomic Characterization.” Frontiers in Public Health 11. https://doi.org/10.3389/fpubh.2023.1198213. \ No newline at end of file diff --git a/docs/workflows/data_export/concatenate_column_content.md b/docs/workflows/data_export/concatenate_column_content.md index 0d6d13347..5534128ef 100644 --- a/docs/workflows/data_export/concatenate_column_content.md +++ b/docs/workflows/data_export/concatenate_column_content.md @@ -6,7 +6,7 @@ title: Concatenate_Column_Content | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Exporting Data From Terra](../../workflows_overview/workflows-type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Set-level | +| [Exporting Data From Terra](../../workflows_overview/workflows_type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Set-level | ## Concatenate_Column_Content_PHB diff --git a/docs/workflows/data_export/transfer_column_content.md b/docs/workflows/data_export/transfer_column_content.md index b76631808..475e4bfb6 100644 --- a/docs/workflows/data_export/transfer_column_content.md +++ b/docs/workflows/data_export/transfer_column_content.md @@ -6,7 +6,7 @@ title: Transfer_Column_Content | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Exporting Data From Terra](../../workflows_overview/workflows-type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Set-level | +| [Exporting Data From Terra](../../workflows_overview/workflows_type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Set-level | ## Transfer_Column_Content_PHB diff --git a/docs/workflows/data_export/zip_column_content.md b/docs/workflows/data_export/zip_column_content.md index 8bce83ebf..3a48f18ad 100644 --- a/docs/workflows/data_export/zip_column_content.md +++ b/docs/workflows/data_export/zip_column_content.md @@ -6,7 +6,7 @@ title: Zip_Column_Content | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** ||||| |---|---|---|---|---| -| [Exporting Data From Terra](../../workflows_overview/workflows-type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Set-level | +| [Exporting Data From Terra](../../workflows_overview/workflows_type.md/#exporting-data-from-terra) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Set-level | ## Zip_Column_Content_PHB diff --git a/docs/workflows/data_import/assembly_fetch.md b/docs/workflows/data_import/assembly_fetch.md index 5f44803b0..9387d0b2e 100644 --- a/docs/workflows/data_import/assembly_fetch.md +++ b/docs/workflows/data_import/assembly_fetch.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Data Import](../../workflows_overview/workflows-type.md/#data-import) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Sample-level | +| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Sample-level | ## Assembly_Fetch_PHB diff --git a/docs/workflows/data_import/basespace_fetch.md b/docs/workflows/data_import/basespace_fetch.md index 5a2db2441..0fe3aa418 100644 --- a/docs/workflows/data_import/basespace_fetch.md +++ b/docs/workflows/data_import/basespace_fetch.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Data Import](../../workflows_overview/workflows-type.md/#data-import) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Sample-level | +| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v1.3.0 | Yes | Sample-level | ## Setting up BaseSpace_Fetch @@ -27,29 +27,29 @@ This process must be performed on a command line (ideally on a Linux or MacOS co 1. Select the "Environment configuration" cloud icon on the right side of the workspace dashboard tab - ![Step1](../../assets/basespace_fetch/step1.png){width="50%"} + ![Step1](../../assets/figures/basespace_fetch/step1.png){width="50%"} 2. Select the "Settings" button under Jupyter - ![Step2](../../assets/basespace_fetch/step2.png){width="50%"} + ![Step2](../../assets/figures/basespace_fetch/step2.png){width="50%"} 3. Click "CREATE" in the "Use default environment section". There is no need to alter the default environment configuration. - ![Step3](../../assets/basespace_fetch/step3.png){width="50%"} + ![Step3](../../assets/figures/basespace_fetch/step3.png){width="50%"} 4. Undertaking steps 1 and 2 again, you will see options to configure the environment. 1. The default environment (default = GATK 4.1.4.1, Python 3.7..10, R 4.0.5) should be sufficient for retrieval of BaseSpace credentials, but if performing other tasks in the environment please modify the resource allocations appropriately. 2. You can use up to 4 CPUs which can help move things faster with multithreaded `gsutil` - ![Step4](../../assets/basespace_fetch/step4.png){width="50%"} + ![Step4](../../assets/figures/basespace_fetch/step4.png){width="50%"} #### Step 2: Install the BaseSpace Command Line Tool To Get The Access Token And API Server Address ??? toggle "Click for more information" 1. Open the "Terminal" app in the right side-bar of the Terra dashboard - ![Step5](../../assets/basespace_fetch/step5.png){width="20%"} + ![Step5](../../assets/figures/basespace_fetch/step5.png){width="20%"} 2. Download and setup BaseSpace (BS) CLI (as per Illumina documentation) by following the commands below. The lines beginning with `#` are comments, the following lines are the commands to be copy/pasted into the termina @@ -80,7 +80,7 @@ This process must be performed on a command line (ideally on a Linux or MacOS co 1. Navigate to the Terra "DATA" tab, and select "Workspace Data" at the bottom left of the page. 2. You can use the ➕ icon to add the new workspace data elements as in the examples below. - ![Step6](../../assets/basespace_fetch/step6.png){width="50%"} + ![Step6](../../assets/figures/basespace_fetch/step6.png){width="50%"} ### Preparing to retrieve a run with BaseSpace_Fetch @@ -96,7 +96,7 @@ This process must be performed on a command line (ideally on a Linux or MacOS co 1. Download the sample sheet from BaseSpace. 1. On the BaseSpace portal, you can navigate to this via: Runs → {run} → Files → SampleSheet.csv - ![Step7](../../assets/basespace_fetch/step7.png){width="50%"} + ![Step7](../../assets/figures/basespace_fetch/step7.png){width="50%"} 2. In Excel, set up a metadata sheet for Terra, with a row for each sample. Please feel free to use our [BaseSpace_Fetch Template](https://storage.googleapis.com/theiagen-public-files/terra/training_resources/bs_fetch_template_20231103.tsv) to help ensure the file is formatted correctly. @@ -109,19 +109,19 @@ This process must be performed on a command line (ideally on a Linux or MacOS co 4. Create a `basespace_collection_id` column, and populate it with the BaseSpace Project or Run identifier 5. Populate column A of the spreadsheet with the sample names - ![Step8](../../assets/basespace_fetch/step8.png){width="50%"} + ![Step8](../../assets/figures/basespace_fetch/step8.png){width="50%"} #### Upload the metadata spreadsheet to the destination workspace in Terra.bio 1. In Terra, navigate to the "DATA" tab, click "IMPORT DATA" then "Upload TSV" - ![Step9](../../assets/basespace_fetch/step9.png){width="25%"} + ![Step9](../../assets/figures/basespace_fetch/step9.png){width="25%"} 2. Copy and paste the contents of the whole spreadsheet into the "TEXT IMPORT" tab and click "START IMPORT JOB" - ![Step10](../../assets/basespace_fetch/step10.png){width="38%"} + ![Step10](../../assets/figures/basespace_fetch/step10.png){width="38%"} ## Using the BaseSpace_Fetch Workflow @@ -138,7 +138,7 @@ This process must be performed on a command line (ideally on a Linux or MacOS co 3. Samples that you wan to import data for. 3. Set up the `BaseSpace_Fetch` "INPUTS" form as below. **Don't forget to fill out `this.basespace_sample_id` if your basespace sample IDs are different from the basespace sample names in the SampleSheet.csv file.** - ![Step11](../../assets/basespace_fetch/step11.png){width="50%"} + ![Step11](../../assets/figures/basespace_fetch/step11.png){width="50%"} 4. In the "OUTPUTS" tab, select "use defaults", then click "SAVE". 5. You can now run the workflow and import data for all the samples you have selected. diff --git a/docs/workflows/data_import/create_terra_table.md b/docs/workflows/data_import/create_terra_table.md index 7497a9143..31c10e024 100644 --- a/docs/workflows/data_import/create_terra_table.md +++ b/docs/workflows/data_import/create_terra_table.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Data Import](../../workflows_overview/workflows-type.md/#data-import) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | +| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | ## Create_Terra_Table_PHB @@ -43,7 +43,7 @@ The manual creation of Terra tables can be tedious and error-prone. This workflo !!! info "Note" If you click "Next" after uploading your files, it will ask for a metadata TSV. You do not have to provide this, and can instead exit the window. Your data will still be uploaded. - ![Data uploader](../../assets/create_terra_table/example1.png) + ![Data uploader](../../assets/figures/Create_Terra_Table_example1.png) #### Using the "Files" section in the Data tab @@ -52,7 +52,7 @@ The manual creation of Terra tables can be tedious and error-prone. This workflo If you uploaded data with the Terra data uploader, your collection will be nested in the "uploads" folder. - ![Data tab](../../assets/create_terra_table/example2.png) + ![Data tab](../../assets/figures/Create_Terra_Table_example2.png) ### How to determine the appropriate `file_ending` for your data diff --git a/docs/workflows/data_import/sra_fetch.md b/docs/workflows/data_import/sra_fetch.md index 34b3a74b8..0b3b407fb 100644 --- a/docs/workflows/data_import/sra_fetch.md +++ b/docs/workflows/data_import/sra_fetch.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Data Import](../../workflows_overview/workflows-type.md/#data-import) | [Any taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | +| [Data Import](../../workflows_overview/workflows_type.md/#data-import) | [Any taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | ## SRA_Fetch_PHB diff --git a/docs/workflows/genomic_characterization/freyja.md b/docs/workflows/genomic_characterization/freyja.md index ac519f9dd..114fcaa1c 100644 --- a/docs/workflows/genomic_characterization/freyja.md +++ b/docs/workflows/genomic_characterization/freyja.md @@ -10,7 +10,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level, Set-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level, Set-level | ## Freyja Overview @@ -23,7 +23,7 @@ Additional post-processing steps can produce visualizations of aggregated sample !!! caption "Figure 1: Workflow Diagram for Freyja_FASTQ_PHB workflow" ##### Figure 1 { #figure1 } - ![**Figure 1: Workflow diagram for Freyja_FASTQ_PHB workflow.**](../../assets/freyja/Freyja_FASTQ.png){width=25%} + ![**Figure 1: Workflow diagram for Freyja_FASTQ_PHB workflow.**](../../assets/figures/Freyja_FASTQ.png){width=25%} Depending on the type of data (Illumina or Oxford Nanopore), the Read QC and Filtering steps, as well as the Read Alignment steps use different software. The user can specify if the barcodes and lineages file should be updated with `freyja update` before running Freyja or if bootstrapping is to be performed with `freyja boot`. @@ -524,13 +524,13 @@ When running **Freyja_FASTQ_PHB**, the appropriate reference and barcodes file n !!! caption "Figure 2: Required input for Freyja_FASTQ_PHB to provide the reference genome to be used by Freyja" ##### Figure 2 { #figure2 } - ![**Figure 2: Required input for Freyja_FASTQ_PHB to provide the reference genome to be used by Freyja.**](../../assets/freyja/figure2.png) + ![**Figure 2: Required input for Freyja_FASTQ_PHB to provide the reference genome to be used by Freyja.**](../../assets/figures/Freyja_figure2.png) The barcodes file can be passed directly to Freyja by the `freyja_usher_barcodes` optional input ([Figure 3](freyja.md/#figure3)). !!! caption "Figure 3: Optional input for Freyja_FASTQ_PHB to provide the barcodes file to be used by Freyja" ##### Figure 3 {#figure3} - ![**Figure 3: Optional input for Freyja_FASTQ_PHB to provide the barcodes file to be used by Freyja.**](../../assets/freyja/figure3.png) + ![**Figure 3: Optional input for Freyja_FASTQ_PHB to provide the barcodes file to be used by Freyja.**](../../assets/figures/Freyja_figure3.png) ## References diff --git a/docs/workflows/genomic_characterization/pangolin_update.md b/docs/workflows/genomic_characterization/pangolin_update.md index b0ba2ac29..b258d2411 100644 --- a/docs/workflows/genomic_characterization/pangolin_update.md +++ b/docs/workflows/genomic_characterization/pangolin_update.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral), SARS-Cov-2 | PHB v2.0.0 | Yes | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral), SARS-Cov-2 | PHB v2.0.0 | Yes | Sample-level | ## Pangolin_Update_PHB diff --git a/docs/workflows/genomic_characterization/theiacov.md b/docs/workflows/genomic_characterization/theiacov.md index 8b909214b..23e512939 100644 --- a/docs/workflows/genomic_characterization/theiacov.md +++ b/docs/workflows/genomic_characterization/theiacov.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.2.0 | Yes, some optional features incompatible | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes, some optional features incompatible | Sample-level | ## TheiaCoV Workflows @@ -51,7 +51,7 @@ Additionally, the **TheiaCoV_FASTA_Batch** workflow is available to process seve - [TheiaCoV_FASTA_RSV-B_2024-04-19.json](https://prod-files-secure.s3.us-west-2.amazonaws.com/be290196-9090-4f3c-a9ab-fe730ad213e0/160cdfbc-a556-40bc-aa05-84ae69511400/TheiaCoV_FASTA_RSV-B_2024-04-19.json) !!! caption "TheiaCoV Workflow Diagram" - ![TheiaCoV Workflow Diagram](../../assets/characterization/TheiaCoV.png) + ![TheiaCoV Workflow Diagram](../../assets/figures/TheiaCoV.png) ### Supported Organisms diff --git a/docs/workflows/genomic_characterization/theiaeuk.md b/docs/workflows/genomic_characterization/theiaeuk.md index 64cdb737d..265479ad6 100644 --- a/docs/workflows/genomic_characterization/theiaeuk.md +++ b/docs/workflows/genomic_characterization/theiaeuk.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibliity** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Mycotics](../../workflows_overview/workflows-kingdom.md/#mycotics) | PHB v2.2.0 | Yes | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Mycotics](../../workflows_overview/workflows_kingdom.md/#mycotics) | PHB v2.2.0 | Yes | Sample-level | ## TheiaEuk Workflows @@ -13,7 +13,7 @@ All input reads are processed through "core tasks" in each workflow. The core tasks include raw-read quality assessment, read cleaning (quality trimming and adapter removal), de novo assembly, assembly quality assessment, and species taxon identification. For some taxa identified, "taxa-specific sub-workflows" will be automatically activated, undertaking additional taxa-specific characterization steps, including clade-typing and/or antifungal resistance detection. !!! caption "TheiaEuk Workflow Diagram" - ![TheiaEuk Workflow Diagram](../../assets/characterization/TheiaEuk_Illumina_PE.png){width=75%} + ![TheiaEuk Workflow Diagram](../../assets/figures/TheiaEuk_Illumina_PE.png){width=75%} ### Inputs @@ -370,7 +370,7 @@ All input reads are processed through "core tasks" in each workflow. The core ta ??? toggle "Template _qc_check_table.tsv_ files" - TheiaEuk_Illumina_PE_PHB: [theiaeuk_qc_check_template.tsv](../../assets/characterization/theiaeuk_qc_check_template.tsv) + TheiaEuk_Illumina_PE_PHB: [theiaeuk_qc_check_template.tsv](../../assets/files/TheiaEuk_qc_check_template.tsv) !!! warning "Example Purposes Only" QC threshold values shown are for example purposes only and should not be presumed to be sufficient for every dataset. diff --git a/docs/workflows/genomic_characterization/theiameta.md b/docs/workflows/genomic_characterization/theiameta.md index 9fcb6b69d..8d0d5c301 100644 --- a/docs/workflows/genomic_characterization/theiameta.md +++ b/docs/workflows/genomic_characterization/theiameta.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.2.0 | Yes | Sample-level | ## TheiaMeta Workflows @@ -17,7 +17,7 @@ TheiaMeta can use one of two distinct methods for generating and processing the !!! caption "TheiaMeta Workflow Diagram" - ![TheiaMeta Workflow Diagram](../../assets/characterization/TheiaMeta_Illumina_PE.png) + ![TheiaMeta Workflow Diagram](../../assets/figures/TheiaMeta_Illumina_PE.png) ### Inputs diff --git a/docs/workflows/genomic_characterization/theiaprok.md b/docs/workflows/genomic_characterization/theiaprok.md index c0a044830..84143af24 100644 --- a/docs/workflows/genomic_characterization/theiaprok.md +++ b/docs/workflows/genomic_characterization/theiaprok.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.2.0 | Yes, some optional features incompatible | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes, some optional features incompatible | Sample-level | ## TheiaProk Workflows @@ -16,7 +16,7 @@ 4. Genome assemblies (**TheiaProk_FASTA**) !!! caption "TheiaProk Workflow Diagram" - ![TheiaProk Workflow Diagram](../../assets/characterization/TheiaProk.png) + ![TheiaProk Workflow Diagram](../../assets/figures/TheiaProk.png) All input reads are processed through "[core tasks](#core-tasks-performed-for-all-taxa)" in the TheiaProk Illumina and ONT workflows. These undertake read trimming and assembly appropriate to the input data type. TheiaProk workflows subsequently launch default genome characterization modules for quality assessment, species identification, antimicrobial resistance gene detection, sequence typing, and more. **For some taxa identified, "taxa-specific sub-workflows" will be automatically activated, undertaking additional taxa-specific characterization steps.** When setting up each workflow, users may choose to use "optional tasks" as additions or alternatives to tasks run in the workflow by default. @@ -1026,8 +1026,8 @@ All input reads are processed through "[core tasks](#core-tasks-performed-for-al ??? toggle "Template _qc_check_table.tsv_ files" - - TheiaProk_Illumina_PE: [theiaprok_illumina_pe_qc_check_template.tsv](../../assets/characterization/theiaprok_illumina_pe_qc_check_template.tsv) - - TheiaProk_FASTA: [theiaprok_fasta_qc_check_template.tsv](../../assets/characterization/theiaprok_fasta_qc_check_template.tsv) + - TheiaProk_Illumina_PE: [theiaprok_illumina_pe_qc_check_template.tsv](../../assets/files/TheiaProk_Illumina_PE_qc_check_template.tsv) + - TheiaProk_FASTA: [theiaprok_fasta_qc_check_template.tsv](../../assets/files/TheiaProk_FASTA_qc_check_template.tsv) !!! warning "Example Purposes Only" QC threshold values shown are for example purposes only and should not be presumed to be sufficient for every dataset. @@ -1472,7 +1472,7 @@ The TheiaProk workflows automatically activate taxa-specific sub-workflows after Global Pneumococcal Sequence Clusters (GPSC) define and name pneumococcal strains. GPSC designation is undertaken using the PopPUNK software and GPSC database as described in the file below, obtained from [here](https://www.pneumogen.net/gps/training_command_line.html). - :file: [GPSC_README_PopPUNK2.txt](../../assets/misc_files/GPSC_README_PopPUNK2.txt) + :file: [GPSC_README_PopPUNK2.txt](../../assets/files/GPSC_README_PopPUNK2.txt) !!! tip "Interpreting GPSC results" - In the `*_external_clusters.csv` novel clusters are assigned NA. For isolates that are assigned a novel cluster and pass QC, you can email [globalpneumoseq@gmail.com](mailto:globalpneumoseq@gmail.com) to have these novel clusters added to the database. diff --git a/docs/workflows/genomic_characterization/vadr_update.md b/docs/workflows/genomic_characterization/vadr_update.md index b5b87dac1..4743222fb 100644 --- a/docs/workflows/genomic_characterization/vadr_update.md +++ b/docs/workflows/genomic_characterization/vadr_update.md @@ -5,7 +5,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Genomic Characterization](../../workflows_overview/workflows-type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v1.2.1 | Yes | Sample-level | +| [Genomic Characterization](../../workflows_overview/workflows_type.md/#genomic-characterization) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v1.2.1 | Yes | Sample-level | ## Vadr_Update_PHB diff --git a/docs/workflows/phylogenetic_construction/augur.md b/docs/workflows/phylogenetic_construction/augur.md index 0183d6a57..7023d6f1f 100644 --- a/docs/workflows/phylogenetic_construction/augur.md +++ b/docs/workflows/phylogenetic_construction/augur.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, Set-level | ## Augur Workflows diff --git a/docs/workflows/phylogenetic_construction/core_gene_snp.md b/docs/workflows/phylogenetic_construction/core_gene_snp.md index 08039f9be..197dcb58e 100644 --- a/docs/workflows/phylogenetic_construction/core_gene_snp.md +++ b/docs/workflows/phylogenetic_construction/core_gene_snp.md @@ -4,12 +4,12 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.1.0 | Yes, some optional features incompatible | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.1.0 | Yes, some optional features incompatible | Set-level | ## Core_Gene_SNP_PHB !!! caption "Core Gene SNP Workflow Diagram" - ![Core Gene SNP Workflow Diagram](../../assets/phylo_diagrams/Core_Gene_SNP.png){width:45%} + ![Core Gene SNP Workflow Diagram](../../assets/figures/Core_Gene_SNP.png){width:45%} The Core_Gene_SNP workflow is intended for pangenome analysis, core gene alignment, and phylogenetic analysis. The workflow takes in gene sequence data in GFF3 format from a set of samples. It first produces a pangenome summary using [`Pirate`](https://github.com/SionBayliss/PIRATE), which clusters genes within the sample set into orthologous gene families. By default, the workflow also instructs `Pirate` to produce both core gene and pangenome alignments. The workflow subsequently triggers the generation of a phylogenetic tree and SNP distance matrix from the core gene alignment using [`iqtree`](https://github.com/iqtree/iqtree2/tree/v1.6.7) and [`snp-dists`](https://github.com/tseemann/snp-dists), respectively. Optionally, the workflow will also run this analysis using the pangenome alignment. This workflow also features an optional module, `summarize_data`, that creates a presence/absence matrix for the analyzed samples from a list of indicated columns (such as AMR genes, etc.) that can be used in Phandango. diff --git a/docs/workflows/phylogenetic_construction/czgenepi_prep.md b/docs/workflows/phylogenetic_construction/czgenepi_prep.md index 46ccb031d..1c2b88804 100644 --- a/docs/workflows/phylogenetic_construction/czgenepi_prep.md +++ b/docs/workflows/phylogenetic_construction/czgenepi_prep.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v1.3.0 | No | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v1.3.0 | No | Set-level | ## CZGenEpi_Prep_PHB diff --git a/docs/workflows/phylogenetic_construction/find_shared_variants.md b/docs/workflows/phylogenetic_construction/find_shared_variants.md index b5ce893a4..49908c0e0 100644 --- a/docs/workflows/phylogenetic_construction/find_shared_variants.md +++ b/docs/workflows/phylogenetic_construction/find_shared_variants.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics) | PHB v2.0.0 | Yes | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) | PHB v2.0.0 | Yes | Set-level | ## Find_Shared_Variants_PHB @@ -12,7 +12,7 @@ !!! caption "Find_Shared_Variants Workflow Diagram" - ![Find_Shared_Variants Workflow Diagram](../../assets/phylo_diagrams/Find_Shared_Variants_PHB.png) + ![Find_Shared_Variants Workflow Diagram](../../assets/figures/Find_Shared_Variants_PHB.png) ### Inputs diff --git a/docs/workflows/phylogenetic_construction/ksnp3.md b/docs/workflows/phylogenetic_construction/ksnp3.md index 39249bbba..e54a0c27b 100644 --- a/docs/workflows/phylogenetic_construction/ksnp3.md +++ b/docs/workflows/phylogenetic_construction/ksnp3.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics), [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.1.0 | Yes; some optional features incompatible | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | Yes; some optional features incompatible | Set-level | ## kSNP3_PHB @@ -82,7 +82,7 @@ If you fill out the `data_summary_*` and `sample_names` optional variables, you Data summary produced using the `phandango_coloring` option, visualized alongside Newick tree at !!! caption "Example phandango_coloring output" - ![Phandango coloring example](../../assets/misc_files/example_phandango_coloring.png) + ![Phandango coloring example](../../assets/figures/example_phandango_coloring.png) ### Outputs diff --git a/docs/workflows/phylogenetic_construction/lyve_set.md b/docs/workflows/phylogenetic_construction/lyve_set.md index 6cbfb2e77..4476cf02b 100644 --- a/docs/workflows/phylogenetic_construction/lyve_set.md +++ b/docs/workflows/phylogenetic_construction/lyve_set.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.1.0 | Yes | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.1.0 | Yes | Set-level | ## Lyve_SET_PHB @@ -13,7 +13,7 @@ The Lyve_SET WDL workflow runs the [Lyve-SET](https://github.com/lskatz/lyve-SET ### Lyve-SET Pipeline (from [Lyve-SET paper](https://www.frontiersin.org/articles/10.3389/fmicb.2017.00375/full)) !!! caption "Lyve-SET Workflow Diagram" - ![Lyve-SET Workflow Diagram](../../assets/phylo_diagrams/lyve_set.png) + ![Lyve-SET Workflow Diagram](../../assets/figures/Lyve_Set.png) ### Inputs diff --git a/docs/workflows/phylogenetic_construction/mashtree_fasta.md b/docs/workflows/phylogenetic_construction/mashtree_fasta.md index 16082f0e7..53ad8f24d 100644 --- a/docs/workflows/phylogenetic_construction/mashtree_fasta.md +++ b/docs/workflows/phylogenetic_construction/mashtree_fasta.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.1.0 | Yes | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.1.0 | Yes | Set-level | ## MashTree_FASTA_PHB diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline.md b/docs/workflows/phylogenetic_construction/snippy_streamline.md index f5f259f4b..7c2fa47df 100644 --- a/docs/workflows/phylogenetic_construction/snippy_streamline.md +++ b/docs/workflows/phylogenetic_construction/snippy_streamline.md @@ -4,13 +4,13 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level | ## Snippy_Streamline_PHB !!! caption "Snippy_Streamline_PHB Workflow Diagram"
- ![Snippy_Streamline_PHB Workflow Diagram](../../assets/phylo_diagrams/Snippy_Streamline.png){width=50%} + ![Snippy_Streamline_PHB Workflow Diagram](../../assets/figures/Snippy_Streamline.png){width=50%}
The `Snippy_Streamline` workflow is an all-in-one approach to generating a reference-based phylogenetic tree and associated SNP-distance matrix. The workflow can be run in multiple ways with options for: diff --git a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md index cf064fde3..11f482891 100644 --- a/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md +++ b/docs/workflows/phylogenetic_construction/snippy_streamline_fasta.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.2.0 | Yes; some optional features incompatible | Set-level | ## Snippy_Streamline_FASTA_PHB @@ -12,7 +12,7 @@ This workflow is a FASTA-compatible version of [Snippy_Streamline](./snippy_stre !!! caption "Snippy_Streamline_FASTA_PHB Workflow Diagram"
- ![Snippy_Streamline_FASTA_PHB Workflow Diagram](../../assets/phylo_diagrams/Snippy_Streamline_FASTA.png){width=50%} + ![Snippy_Streamline_FASTA_PHB Workflow Diagram](../../assets/figures/Snippy_Streamline_FASTA.png){width=50%}
The `Snippy_Streamline_FASTA` workflow is an all-in-one approach to generating a reference-based phylogenetic tree and associated SNP-distance matrix. The workflow can be run in multiple ways with options for: diff --git a/docs/workflows/phylogenetic_construction/snippy_tree.md b/docs/workflows/phylogenetic_construction/snippy_tree.md index e68a8d7bf..9f643803d 100644 --- a/docs/workflows/phylogenetic_construction/snippy_tree.md +++ b/docs/workflows/phylogenetic_construction/snippy_tree.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.1.0 | Yes; some optional features incompatible | Set-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.1.0 | Yes; some optional features incompatible | Set-level | ## Snippy_Tree_PHB @@ -256,7 +256,7 @@ Sequencing data used in the Snippy_Tree workflow must: Data summary produced using the `phandango_coloring` option, visualized alongside Newick tree at !!! caption "Example phandango_coloring output" - ![Phandango coloring example](../../assets/misc_files/example_phandango_coloring.png) + ![Phandango coloring example](../../assets/figures/example_phandango_coloring.png) !!! techdetails "Data summary technical details" diff --git a/docs/workflows/phylogenetic_construction/snippy_variants.md b/docs/workflows/phylogenetic_construction/snippy_variants.md index bda23f45a..9f62e6018 100644 --- a/docs/workflows/phylogenetic_construction/snippy_variants.md +++ b/docs/workflows/phylogenetic_construction/snippy_variants.md @@ -4,14 +4,14 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Construction](../../workflows_overview/workflows-type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics), [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level | +| [Phylogenetic Construction](../../workflows_overview/workflows_type.md/#phylogenetic-construction) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics), [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Sample-level | ## Snippy_Variants_PHB The `Snippy_Variants` workflow aligns single-end or paired-end reads (in FASTQ format), or assembled sequences (in FASTA format), against a reference genome, then identifies single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and insertions/deletions (INDELs) across the alignment. If a GenBank file is used as the reference, mutations associated with user-specified query strings (e.g. genes of interest) can additionally be reported to the Terra data table. !!! caption "Snippy_Variants Workflow Diagram" - ![Snippy_Variants Workflow Diagram](../../assets/phylo_diagrams/Snippy_Variants.png) + ![Snippy_Variants Workflow Diagram](../../assets/figures/Snippy_Variants.png) !!! tip "Example Use Cases" - **Finding mutations** (SNPs, MNPs, and INDELs) in your own sample's reads relative to a reference, e.g. mutations in genes of phenotypic interest. diff --git a/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md b/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md index e53c61233..308b02b60 100644 --- a/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md +++ b/docs/workflows/phylogenetic_placement/samples_to_ref_tree.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Placement](../../workflows_overview/workflows-type.md/#phylogenetic-placement) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, Set-level | +| [Phylogenetic Placement](../../workflows_overview/workflows_type.md/#phylogenetic-placement) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, Set-level | ## Samples_to_Ref_Tree_PHB diff --git a/docs/workflows/phylogenetic_placement/usher.md b/docs/workflows/phylogenetic_placement/usher.md index cb53c0348..ccd09f92f 100644 --- a/docs/workflows/phylogenetic_placement/usher.md +++ b/docs/workflows/phylogenetic_placement/usher.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Phylogenetic Placement](../../workflows_overview/workflows-type.md/#phylogenetic-placement) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, set-level | +| [Phylogenetic Placement](../../workflows_overview/workflows_type.md/#phylogenetic-placement) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | Yes | Sample-level, set-level | ## Usher_PHB diff --git a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md index 123653ff9..4d5029e43 100644 --- a/docs/workflows/public_data_sharing/mercury_prep_n_batch.md +++ b/docs/workflows/public_data_sharing/mercury_prep_n_batch.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Public Data Sharing](../../workflows_overview/workflows-type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.2.0 | Yes | Set-level | +| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.2.0 | Yes | Set-level | ## Mercury_Prep_N_Batch_PHB @@ -123,7 +123,7 @@ This workflow runs on the set-level. Due to the nature of tsv files, it may be easier to download and open this file in Excel. - [example_excluded_samples.tsv](../../assets/misc_files/example_excluded_samples.tsv) + [example_excluded_samples.tsv](../../assets/files/example_excluded_samples.tsv) ``` Samples excluded for quality thresholds: diff --git a/docs/workflows/public_data_sharing/terra_2_gisaid.md b/docs/workflows/public_data_sharing/terra_2_gisaid.md index 49f567712..902521641 100644 --- a/docs/workflows/public_data_sharing/terra_2_gisaid.md +++ b/docs/workflows/public_data_sharing/terra_2_gisaid.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Public Data Sharing](../../workflows_overview/workflows-type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v1.2.1 | Yes | Set-level | +| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v1.2.1 | Yes | Set-level | ## Terra_2_GISAID_PHB diff --git a/docs/workflows/public_data_sharing/terra_2_ncbi.md b/docs/workflows/public_data_sharing/terra_2_ncbi.md index 73b0eb12d..c64b41f05 100644 --- a/docs/workflows/public_data_sharing/terra_2_ncbi.md +++ b/docs/workflows/public_data_sharing/terra_2_ncbi.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Public Data Sharing](../../workflows_overview/workflows-type.md/#public-data-sharing) | [Bacteria](../../workflows_overview/workflows-kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics) [Viral](../../workflows_overview/workflows-kingdom.md/#viral) | PHB v2.1.0 | No | Set-level | +| [Public Data Sharing](../../workflows_overview/workflows_type.md/#public-data-sharing) | [Bacteria](../../workflows_overview/workflows_kingdom.md#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) [Viral](../../workflows_overview/workflows_kingdom.md/#viral) | PHB v2.1.0 | No | Set-level | ## Terra_2_NCBI_PHB @@ -199,7 +199,7 @@ The output files contain information mostly for debugging purposes. Additionally Due to the nature of tsv files, it may be easier to download and open this file in Excel. - [example_excluded_samples.tsv](../../assets/misc_files/example_excluded_samples.tsv) + [example_excluded_samples.tsv](../../assets/files/example_excluded_samples.tsv) ``` Samples excluded for quality thresholds: diff --git a/docs/workflows/standalone/cauris_cladetyper.md b/docs/workflows/standalone/cauris_cladetyper.md index 2fe611f0a..eca2023ec 100644 --- a/docs/workflows/standalone/cauris_cladetyper.md +++ b/docs/workflows/standalone/cauris_cladetyper.md @@ -7,7 +7,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics) | PHB v1.0.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) | PHB v1.0.0 | Yes | Sample-level | ## Cauris_CladeTyper_PHB diff --git a/docs/workflows/standalone/gambit_query.md b/docs/workflows/standalone/gambit_query.md index 55176fb56..b49f76083 100644 --- a/docs/workflows/standalone/gambit_query.md +++ b/docs/workflows/standalone/gambit_query.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics) | PHB v2.2.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) | PHB v2.2.0 | Yes | Sample-level | ## GAMBIT_Query_PHB diff --git a/docs/workflows/standalone/kraken2.md b/docs/workflows/standalone/kraken2.md index 300a0ea52..e87353c4e 100644 --- a/docs/workflows/standalone/kraken2.md +++ b/docs/workflows/standalone/kraken2.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level | ## Kraken2 Workflows @@ -21,7 +21,7 @@ There are three Kraken2 workflows: Besides the data input types, there are minimal differences between these two workflows. !!! caption "Kraken2 Workflow Diagram" - ![Kraken2 Workflow Diagram](../../assets/standalone/Kraken2.png) + ![Kraken2 Workflow Diagram](../../assets/figures/Kraken2.png) ### Databases @@ -139,7 +139,7 @@ Krona will only output hierarchical results for bacterial organisms in its curre Below is an example of the `krona_html` for a metagenomic sample. Taxonomic rank is organised from the centre of the pie chart to the edge, with each slice representing the relative abundance of a given taxa in the sample. - ![Example Krona Report](../../assets/misc_files/example_krona_report.png) + ![Example Krona Report](../../assets/figures/example_krona_report.png) !!! techdetails "Kraken2 Technical Details" | | Links | diff --git a/docs/workflows/standalone/ncbi_amrfinderplus.md b/docs/workflows/standalone/ncbi_amrfinderplus.md index dc8ac61ee..237e79039 100644 --- a/docs/workflows/standalone/ncbi_amrfinderplus.md +++ b/docs/workflows/standalone/ncbi_amrfinderplus.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows-kingdom.md#mycotics) | PHB v2.2.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria), [Mycotics](../../workflows_overview/workflows_kingdom.md#mycotics) | PHB v2.2.0 | Yes | Sample-level | ## NCBIAMRFinderPlus_PHB diff --git a/docs/workflows/standalone/rasusa.md b/docs/workflows/standalone/rasusa.md index ae513909c..055b235f5 100644 --- a/docs/workflows/standalone/rasusa.md +++ b/docs/workflows/standalone/rasusa.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.0.0 | Yes | Sample-level | ## RASUSA_PHB diff --git a/docs/workflows/standalone/rename_fastq.md b/docs/workflows/standalone/rename_fastq.md index 531a3b6ee..19ec4b4a6 100644 --- a/docs/workflows/standalone/rename_fastq.md +++ b/docs/workflows/standalone/rename_fastq.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.1.0 | Yes | Sample-level | ## Rename_FASTQ_PHB diff --git a/docs/workflows/standalone/tbprofiler_tngs.md b/docs/workflows/standalone/tbprofiler_tngs.md index 1b23bd778..3e505cabb 100644 --- a/docs/workflows/standalone/tbprofiler_tngs.md +++ b/docs/workflows/standalone/tbprofiler_tngs.md @@ -4,7 +4,7 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Bacteria](../../workflows_overview/workflows-kingdom.md/#bacteria) | PHB v2.0.0 | Yes | Sample-level | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Bacteria](../../workflows_overview/workflows_kingdom.md/#bacteria) | PHB v2.0.0 | Yes | Sample-level | ## TBProfiler_tNGS_PHB diff --git a/docs/workflows/standalone/theiavalidate.md b/docs/workflows/standalone/theiavalidate.md index d10096a8d..9aee82b32 100644 --- a/docs/workflows/standalone/theiavalidate.md +++ b/docs/workflows/standalone/theiavalidate.md @@ -4,12 +4,12 @@ | **Workflow Type** | **Applicable Kingdom** | **Last Known Changes** | **Command-line Compatibility** | **Workflow Level** | |---|---|---|---|---| -| [Standalone](../../workflows_overview/workflows-type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows-kingdom.md/#any-taxa) | PHB v2.0.0 | No | | +| [Standalone](../../workflows_overview/workflows_type.md/#standalone) | [Any Taxa](../../workflows_overview/workflows_kingdom.md/#any-taxa) | PHB v2.0.0 | No | | ## TheiaValidate_PHB !!! caption "TheiaValidate Workflow Diagram" - ![TheiaValidate Workflow Diagram](../../assets/theiavalidate/TheiaValidate.png) + ![TheiaValidate Workflow Diagram](../../assets/figures/TheiaValidate.png) TheiaValidate performs basic comparisons between user-designated columns in two separate tables. We anticipate this workflow being run to determine if any differences exist between version releases or two workflows, such as TheiaProk_ONT vs TheiaProk_Illumina_PE. A summary PDF report is produced in addition to a Excel spreadsheet that lists the values for any columns that do not have matching content for a sample. @@ -21,9 +21,9 @@ In order to enable this workflow to function for different workflow series, we r !!! tool "Validation Starting Points" | Workflow Series | Validation Criteria TSV | Columns to Compare | |---|---|---| - | TheiaCoV Workflows | [TheiaCov Validation Criteria](../../assets/theiavalidate/theiacov-validation-criteria.txt) | abricate_flu_subtype,abricate_flu_type,assembly_length_unambiguous,assembly_mean_coverage,irma_subtype,irma_type,kraken_human,kraken_human_dehosted,kraken_sc2,kraken_sc2_dehosted,kraken_target_org,kraken_target_org_dehosted,nextclade_aa_dels,nextclade_aa_subs,nextclade_clade,nextclade_lineage,nextclade_tamiflu_resistance_aa_subs,num_reads_clean1,num_reads_clean2,number_N,pango_lineage,percent_reference_coverage,vadr_num_alerts | - | TheiaEuk Workflows | [TheiaEuk Validation Criteria](../../assets/theiavalidate/theiaeuk-validation-criteria.txt) | assembly_length,busco_results,clade_type,est_coverage_clean,est_coverage_raw,gambit_predicted_taxon,n50_value,num_reads_clean1,num_reads_clean2,number_contigs,quast_gc_percent,theiaeuk_snippy_variants_hits | - | TheiaProk Workflows | [TheiaProk Validation Criteria](../../assets/theiavalidate/theiaprok-validation-criteria.txt) | abricate_abaum_plasmid_type_genes,agrvate_agr_group,amrfinderplus_amr_core_genes,amrfinderplus_amr_plus_genes,amrfinderplus_stress_genes,amrfinderplus_virulence_genes,ani_highest_percent,ani_top_species_match,assembly_length,busco_results,ectyper_predicted_serotype,emmtypingtool_emm_type,est_coverage_clean,est_coverage_raw,gambit_predicted_taxon,genotyphi_final_genotype,hicap_genes,hicap_serotype,kaptive_k_type,kleborate_genomic_resistance_mutations,kleborate_key_resistance_genes,kleborate_mlst_sequence_type,legsta_predicted_sbt,lissero_serotype,meningotype_serogroup,midas_primary_genus,midas_secondary_genus,midas_secondary_genus_abundance,n50_value,ngmaster_ngmast_sequence_type,ngmaster_ngstar_sequence_type,num_reads_clean1,num_reads_clean2,number_contigs,pasty_serogroup,pbptyper_predicted_1A_2B_2X,plasmidfinder_plasmids,poppunk_gps_cluster,seqsero2_predicted_serotype,seroba_ariba_serotype,seroba_serotype,serotypefinder_serotype,shigatyper_ipaB_presence_absence,shigatyper_predicted_serotype,shigeifinder_cluster,shigeifinder_serotype,sistr_predicted_serotype,sonneityping_final_genotype,spatyper_type,srst2_vibrio_serogroup,staphopiasccmec_types_and_mecA_presence,tbprofiler_main_lineage,tbprofiler_resistance_genes,ts_mlst_predicted_st,virulencefinder_hits | + | TheiaCoV Workflows | [TheiaCov Validation Criteria](../../assets/files/theiavalidate/theiacov-validation-criteria.txt) | abricate_flu_subtype,abricate_flu_type,assembly_length_unambiguous,assembly_mean_coverage,irma_subtype,irma_type,kraken_human,kraken_human_dehosted,kraken_sc2,kraken_sc2_dehosted,kraken_target_org,kraken_target_org_dehosted,nextclade_aa_dels,nextclade_aa_subs,nextclade_clade,nextclade_lineage,nextclade_tamiflu_resistance_aa_subs,num_reads_clean1,num_reads_clean2,number_N,pango_lineage,percent_reference_coverage,vadr_num_alerts | + | TheiaEuk Workflows | [TheiaEuk Validation Criteria](../../assets/files/theiavalidate/theiaeuk-validation-criteria.txt) | assembly_length,busco_results,clade_type,est_coverage_clean,est_coverage_raw,gambit_predicted_taxon,n50_value,num_reads_clean1,num_reads_clean2,number_contigs,quast_gc_percent,theiaeuk_snippy_variants_hits | + | TheiaProk Workflows | [TheiaProk Validation Criteria](../../assets/files/theiavalidate/theiaprok-validation-criteria.txt) | abricate_abaum_plasmid_type_genes,agrvate_agr_group,amrfinderplus_amr_core_genes,amrfinderplus_amr_plus_genes,amrfinderplus_stress_genes,amrfinderplus_virulence_genes,ani_highest_percent,ani_top_species_match,assembly_length,busco_results,ectyper_predicted_serotype,emmtypingtool_emm_type,est_coverage_clean,est_coverage_raw,gambit_predicted_taxon,genotyphi_final_genotype,hicap_genes,hicap_serotype,kaptive_k_type,kleborate_genomic_resistance_mutations,kleborate_key_resistance_genes,kleborate_mlst_sequence_type,legsta_predicted_sbt,lissero_serotype,meningotype_serogroup,midas_primary_genus,midas_secondary_genus,midas_secondary_genus_abundance,n50_value,ngmaster_ngmast_sequence_type,ngmaster_ngstar_sequence_type,num_reads_clean1,num_reads_clean2,number_contigs,pasty_serogroup,pbptyper_predicted_1A_2B_2X,plasmidfinder_plasmids,poppunk_gps_cluster,seqsero2_predicted_serotype,seroba_ariba_serotype,seroba_serotype,serotypefinder_serotype,shigatyper_ipaB_presence_absence,shigatyper_predicted_serotype,shigeifinder_cluster,shigeifinder_serotype,sistr_predicted_serotype,sonneityping_final_genotype,spatyper_type,srst2_vibrio_serogroup,staphopiasccmec_types_and_mecA_presence,tbprofiler_main_lineage,tbprofiler_resistance_genes,ts_mlst_predicted_st,virulencefinder_hits | If additional validation metrics are desired, the user has the ability to provide a `validation_criteria_tsv` file that specifies what type of comparison should be performed. There are several options for additional validation checks: @@ -147,12 +147,12 @@ To help demonstrate how TheiaValidate works, please observe the following exampl If the above inputs are provided, then the following output files will be generated: -[filtered_example_table1.tsv](../../assets/theiavalidate/filtered_example_table1.tsv) +[filtered_example_table1.tsv](../../assets/files/theiavalidate/filtered_example_table1.tsv) -[filtered_example_table2.tsv](../../assets/theiavalidate/filtered_example_table2.tsv) +[filtered_example_table2.tsv](../../assets/files/theiavalidate/filtered_example_table2.tsv) -[example_summary.pdf](../../assets/theiavalidate/example_summary.pdf) +[example_summary.pdf](../../assets/files/theiavalidate/example_summary.pdf) -[example_exact_differences.tsv](../../assets/theiavalidate/example_exact_differences.tsv) +[example_exact_differences.tsv](../../assets/files/theiavalidate/example_exact_differences.tsv) -[example_validation_criteria_differences.tsv](../../assets/theiavalidate/example_validation_criteria_differences.tsv) \ No newline at end of file +[example_validation_criteria_differences.tsv](../../assets/files/theiavalidate/example_validation_criteria_differences.tsv) \ No newline at end of file diff --git a/docs/workflows_overview/workflows-alphabetically.md b/docs/workflows_overview/workflows_alphabetically.md similarity index 99% rename from docs/workflows_overview/workflows-alphabetically.md rename to docs/workflows_overview/workflows_alphabetically.md index c97da1bc9..0111bab8b 100644 --- a/docs/workflows_overview/workflows-alphabetically.md +++ b/docs/workflows_overview/workflows_alphabetically.md @@ -2,7 +2,7 @@ title: Alphabetical Workflows --- -[Sort by Workflow Type](workflows-type.md) | [Sort by Kingdom](workflows-kingdom.md) +[Sort by Workflow Type](workflows_type.md) | [Sort by Kingdom](workflows_kingdom.md) --- diff --git a/docs/workflows_overview/workflows-kingdom.md b/docs/workflows_overview/workflows_kingdom.md similarity index 99% rename from docs/workflows_overview/workflows-kingdom.md rename to docs/workflows_overview/workflows_kingdom.md index db18c58a4..095c8a170 100644 --- a/docs/workflows_overview/workflows-kingdom.md +++ b/docs/workflows_overview/workflows_kingdom.md @@ -2,7 +2,7 @@ title: Workflows by Kingdom --- -[Sort by Type](workflows-type.md) | [Sort Alphabetically](workflows-alphabetically.md) +[Sort by Type](workflows_type.md) | [Sort Alphabetically](workflows_alphabetically.md) --- diff --git a/docs/workflows_overview/workflows-type.md b/docs/workflows_overview/workflows_type.md similarity index 99% rename from docs/workflows_overview/workflows-type.md rename to docs/workflows_overview/workflows_type.md index bb7af9a7d..1fb16c7c3 100644 --- a/docs/workflows_overview/workflows-type.md +++ b/docs/workflows_overview/workflows_type.md @@ -2,7 +2,7 @@ title: Workflows by Type --- -[Sort by Kingdom](workflows-kingdom.md) | [Sort Alphabetically](workflows-alphabetically.md) +[Sort by Kingdom](workflows_kingdom.md) | [Sort Alphabetically](workflows_alphabetically.md) --- diff --git a/mkdocs.yml b/mkdocs.yml index a042b6ffe..8b7896f20 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -8,9 +8,12 @@ repo_url: https://github.com/theiagen/public_health_bioinformatics nav: - Public Health Bioinformatics: - index.md - - All Workflows: + - Getting Started: + - With the Command-Line: getting_started/commandline.md + - With Terra.bio: getting_started/terra.md + - Workflows: - Workflows by Type: - - Overview Table: workflows_overview/workflows-type.md + - Overview Table: workflows_overview/workflows_type.md - Data Import: - Assembly_Fetch: workflows/data_import/assembly_fetch.md - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md @@ -57,7 +60,7 @@ nav: - TBProfiler_tNGS: workflows/standalone/tbprofiler_tngs.md - TheiaValidate: workflows/standalone/theiavalidate.md - Workflows by Kingdom: - - Overview Table: workflows_overview/workflows-kingdom.md + - Overview Table: workflows_overview/workflows_kingdom.md - Any Taxa: - Assembly_Fetch: workflows/data_import/assembly_fetch.md - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md @@ -112,7 +115,7 @@ nav: - Usher_PHB: workflows/phylogenetic_placement/usher.md - VADR_Update: workflows/genomic_characterization/vadr_update.md - Workflows Alphabetically: - - Overview Table: workflows_overview/workflows-alphabetically.md + - Overview Table: workflows_overview/workflows_alphabetically.md - Assembly_Fetch: workflows/data_import/assembly_fetch.md - Augur: workflows/phylogenetic_construction/augur.md - BaseSpace_Fetch: workflows/data_import/basespace_fetch.md @@ -151,13 +154,13 @@ nav: - Usher_PHB: workflows/phylogenetic_placement/usher.md - VADR_Update: workflows/genomic_characterization/vadr_update.md - Zip_Column_Content: workflows/data_export/zip_column_content.md - - Contributing to the Documentation: contribution_guide.md - - Contributing to the Code: code_contribution.md + - Contributing to the Documentation: contributing/doc_contribution.md + - Contributing to the Code: contributing/code_contribution.md theme: name: material - logo: assets/Theiagen-Logo-White.png - favicon: assets/Theiagen-Symbol-Standard-01.png + logo: assets/logos/Theiagen-Logo-White.png + favicon: assets/logos/Theiagen-Symbol-Standard-01.png custom_dir: docs/overrides features: - content.code.annotate