add sops and format the getting starteds

docs/index.md

@@ -1,17 +1,40 @@
 ---
-title: Overview
+title: Home
 ---
 
-## Documentation and Resources
+## Purpose & Workflows
 
-Theiagen's approach to genomic analysis in public health typically uses the [Terra](https://terra.bio/) platform to run workflows that undertake bioinformatic analysis, then uses other platforms for visualization of the resulting data. Theiagen's **Public Health Bioinformatics (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.
+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.
+
+<center>[Explore our workflows](workflows_overview/workflows_type.md){ .md-button .md-button--primary }</center>
+
+<div class="grid cards " markdown>
+
+-   <center>[Command-line Users](getting_started/commandline.md){ .md-button .md-button--secondary }</center>
+
+    ---
+
+    Learn how to use our workflows on the command-line!
+
+-   <center>[Terra Users](getting_started/terra.md){ .md-button .md-button--secondary }</centered>
+
+    ---
+
+    Learn how to use our workflows on Terra!
+
+</div>
 
 !!! dna "Our Open Source Philosophy"
-    PHB source code is publicly available on [GitHub](https://github.com/theiagen/public_health_bioinformatics)!
+    PHB source code is publicly available on [GitHub](https://github.com/theiagen/public_health_bioinformatics) and available under [GNU Affero General Public License v3.0](https://github.com/theiagen/public_health_viral_genomics/blob/main/LICENSE)!
 
-    All workflows can be imported directly to [Terra](https://terra.bio/) via the [**Dockstore PHB collection**](https://dockstore.org/organizations/Theiagen/collections/public-health-bioinformatics)!
+    All workflows can be imported directly to [Terra](https://terra.bio/) via the [**Dockstore PHB collection**](https://dockstore.org/organizations/Theiagen/collections/public-health-bioinformatics)! 
+
+    You can also use our workflows on the command-line. Please see our guide on how to get started [**here**](getting_started/commandline.md)!
 
-**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.**
+When undertaking genomic analysis using the command-line, via Terra, or 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/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."}
@@ -24,83 +47,75 @@ Theiagen's approach to genomic analysis in public health typically uses the [Ter
 We continuously work to improve our codebase and usability of our workflows by the public health community, so changes from version to version are expected.  This documentation page reflects the state of the workflow at the version stated in the title.
 
 !!! dna "What's new?"
-    You can see the changes since PHB v2.0.1 [**here**](https://www.notion.so/Public-Health-Bioinformatics-v2-1-0-Minor-Release-Notes-e4eb83259b744ca591fc5a6c4d53f977?pvs=21)!
-
-Our code is open-source and available under [GNU Affero General Public License v3.0](https://github.com/theiagen/public_health_viral_genomics/blob/main/LICENSE)
+    You can see the changes since PHB v2.1.0 [**here**](https://theiagen.notion.site/Public-Health-Bioinformatics-v2-2-0-Minor-Release-Notes-9b2781f27b8d4b69949f8fc1ef04868d?pvs=4)!
 
-----
+## Contributing to the PHB Repository
 
-### Contributing to the PHB Repository
+We warmly welcome contributions to this repository! Our style guide may be found [here](contributing/code_contribution.md) for convenience of formatting.
 
 If you would like to submit suggested code changes to our workflows, you may add or modify the WDL files and submit pull requests to the [PHB GitHub](https://github.com/theiagen/public_health_bioinformatics) repository.
 
-### About Theiagen
+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
 
-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/).
+### Authorship
 
-------
+(Ordered by contribution [# of lines changed] as of 2024-08-01)
 
-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.
+- **Sage Wright** ([@sage-wright](https://github.com/sage-wright)) - Conceptualization, Software, Validation, Supervision
+- **Inês Mendes** ([@cimendes](https://github.com/cimendes)) - Software, Validation
+- **Curtis Kapsak** ([@kapsakcj](https://github.com/kapsakcj)) - Conceptualization, Software, Validation
+- **James Otieno** ([@jrotieno](https://github.com/jrotieno)) - Software, Validation
+- **Frank Ambrosio** ([@frankambrosio3](https://github.com/frankambrosio3)) - Conceptualization, Software, Validation
+- **Michelle Scribner** ([@michellescribner](https://github.com/michellescribner)) - Software, Validation
+- **Kevin Libuit** ([@kevinlibuit](https://github.com/kevinlibuit)) - Conceptualization, Project Administration, Software, Validation, Supervision
+- **Emma Doughty** ([@emmadoughty](https://github.com/emmadoughty)) - Software, Validation
+- **Andrew Page** ([@andrewjpage](https://github.com/andrewjpage)) - Project Administration, Software, Supervision
+- **Andrew Lang** ([@AndrewLangVt](https://github.com/AndrewLangVt)) - Software, Supervision
+- **Kelsey Kropp** ([@kelseykropp](https://github.com/kelseykropp)) - Validation
+- **Emily Smith** ([@emily-smith1](https://github.com/emily-smith1)) - Validation
+- **Joel Sevinsky** ([@sevinsky](https://github.com/sevinsky)) - Conceptualization, Project Administration, Supervision
+
+### External Contributors
 
-All workflows in the PHB repository end with _PHB in order to differentiate them from earlier versions and from the original tools they incorporate.
+We would like to gratefully acknowledge the following individuals from the public health community for their contributions to the PHB repository:
 
-Briefly, the main genomic characterization workflows are split by pathogen type:
+- **Robert Petit** ([@rpetit3](https://github.com/rpetit3))
+- **Ash O'Farrel** ([@aofarrel](https://github.com/aofarrel))
+- **Sam Baird** ([@sam-baird](https://github.com/sam-baird))
+- **Holly Halstead** ([@HNHalstead](https://github.com/HNHalstead))
 
-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
 
-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.
+The PHB repository originated from collaborative work with Andrew Lang, PhD & his [Genomic Analysis WDL workflows](https://github.com/AndrewLangvt/genomic_analyses). The workflows and task development were influenced by The Broad's [Viral Pipes](https://github.com/broadinstitute/viral-pipelines) repository. The TheiaCoV workflows for viral genomic characterization were influenced by UPHL's [Cecret](https://github.com/UPHL-BioNGS/Cecret) & StaPH-B's [Monroe](https://staph-b.github.io/staphb_toolkit/workflow_docs/monroe/) workflows. The TheiaProk workflows for bacterial genomic characterization were influenced by Robert Petit's [bactopia](https://github.com/bactopia/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.
+If you would like to provide feedback, please raise a [GitHub issue](https://github.com/theiagen/public_health_bioinformatics/issues/new) or contact us at <[email protected]>.
 
-Contributing to the PHB workflows
-We warmly welcome contributions to this repository! Our style guide may be found here for convenience of formatting.
+### Maintaining PHB Pipelines
 
-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!
+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](https://github.com/StaPH-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.
 
-Authorship & Responsibility
-Authorship
-(Ordered by contribution [# of lines changed] as of 2024-08-01)
+### Point of Contact
 
-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.
+If you have any questions or concerns, please raise a [GitHub issue](https://github.com/theiagen/public_health_bioinformatics/issues/new) or email Theiagen's general support at <[email protected]>.
 
-Point of Contact
-If you have any questions or concerns, please raise a GitHub issue or email Theiagen's general support at [email protected].
+### Conflict of Interest
 
-Conflict of Interest
 The authors declare no conflict of interest.
 
-Citation
+## 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.
+> 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.
+> 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>.
+
+## 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/).

docs/overrides/main.html

@@ -5,4 +5,16 @@
   <a href="{{ '../' ~ base_url }}"> 
     <strong>Click here to go to the latest version release.</strong>
   </a>
-{% endblock %}
+{% endblock %}
+
+
+<!-- REMOVE WHEN DOCUMENTATION IS FINALIZED -->
+{% block header %}
+
+<div class="banner">
+    <p style="color:#ffffff; display:inline;">🏗️ I'm under construction! Pardon the dust while we remodel! 👷</p>
+</div>
+
+<!-- Original Header -->
+{% include "partials/header.html" %}
+{% endblock %}

docs/stylesheets/extra.css

@@ -2,8 +2,8 @@
 [data-md-color-scheme="light"] {
   --md-primary-bg-color: #ffffff;
   --md-primary-fg-color: #116eb7;
+  --md-accent-bg-color: #ffffff;
   --md-accent-fg-color: #1da74a;
-  --md-accent-bg-color: #1da74a;
   th {
     background: #ffffff;
     color: #262626;
@@ -20,8 +20,8 @@
 [data-md-color-scheme="slate"] {
   --md-primary-bg-color: #1da74a;
   --md-primary-fg-color: #262626;
+  --md-accent-bg-color: #ffffff;
   --md-accent-fg-color: #1da74a;
-  --md-accent-bg-color: #116eb7;
   th {
     background: #1F2029;
     color: #ffffff;
@@ -155,6 +155,15 @@
   position: relative;
 }
 
+/* edit the tip admonition */
+.md-typeset .tip > h5 {
+  /* this renders the heading readable by screen readers but does not display it */
+  margin: -1px; padding: 0; border: 0; 
+  visibility: hidden;
+  margin-top: -15px; /* this makes the header in the TOC jump to the top of the admonition box */
+  position: relative;
+}
+
 /* content width */
 .md-grid {
   max-width: initial;
@@ -175,3 +184,24 @@ th {
 td {
   word-break: break-all;
 }
+
+
+
+/* UNDER CONSTRUCTION ANNOUNCEMENT; comment out when needing removal */
+.banner {
+  height: 30px;       /* Height of the banner */
+  line-height: 30px;  /* Center the text vertically */
+  position: sticky;   /* Follows as you scroll */
+  top: 0;             /* Absolute top of page */
+  left: 0;
+  width: 100%;
+  z-index: 1;         /* Tells the renderer "this is important", otherwise Admonition and Code Blocks will render into it */
+  text-align: center;
+  vertical-align: middle;
+  font-size: 14pt;
+  background-color: #262626;
+}
+
+.md-header {
+  top: 30px;          /* This setting prevents the Material header from imposing into the space of the banner! */
+}