Merge branch 'main' into fc-dorado-workflow-standalone-dev

.gitignore

@@ -1,3 +1,4 @@
 cromwell*
 _LAST
-2024*
+2024*site/
+site/

README.md

@@ -28,7 +28,7 @@ Many more workflows are available, and are documented in detail in the [Theiagen
 
 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](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.
+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 (now deprecated) 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](https://github.com/theiagen/public_health_bioinformatics/issues/new).
 

docs/assets/files/input_jsons/TheiaCoV_FASTA_RSV-A_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_fasta.organism":"rsv_a"}

docs/assets/files/input_jsons/TheiaCoV_FASTA_RSV-B_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_fasta.organism":"rsv_b"}

docs/assets/files/input_jsons/TheiaCoV_FASTA_WNV_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_fasta.organism":"WNV"}

docs/assets/files/input_jsons/TheiaCoV_FASTA_flu_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_fasta.organism":"flu"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_HIV_v1_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"HIV","theiacov_illumina_pe.hiv_primer_version":"v1"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_HIV_v2_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"HIV","theiacov_illumina_pe.hiv_primer_version":"v2"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_RSV-A_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"rsv_a"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_RSV-B_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"rsv_b"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_WNV_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"WNV"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_PE_flu_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_pe.organism":"flu"}

docs/assets/files/input_jsons/TheiaCoV_Illumina_SE_WNV_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_illumina_se.organism":"WNV"}

docs/assets/files/input_jsons/TheiaCoV_ONT_HIV_v1_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_ont.organism":"HIV","theiacov_ont.hiv_primer_version":"v1"}

docs/assets/files/input_jsons/TheiaCoV_ONT_HIV_v2_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_ont.organism":"HIV","theiacov_ont.hiv_primer_version":"v2"}

docs/assets/files/input_jsons/TheiaCoV_ONT_flu_2024-04-19.json

@@ -0,0 +1 @@
+{"theiacov_ont.organism":"flu"}

docs/contributing/doc_contribution.md

@@ -34,6 +34,7 @@ Here are some VSCode Extensions can help you write and edit your markdown files
 
 - [Excel to Markdown Table](https://tableconvert.com/excel-to-markdown) - This website will convert an Excel table into markdown format, which can be copied and pasted into your markdown file.
 - [Material for MkDocs Reference](https://squidfunk.github.io/mkdocs-material/reference/) - This is the official reference for the Material for MkDocs theme, which will help you understand how to use the theme's features.
+- [Broken Link Check](https://www.brokenlinkcheck.com/) - This website will scan your website to ensure that all links are working correctly. This will only work on the deployed version of the documentation, not the local version.
 
 ## Documentation Structure
 

docs/index.md

@@ -6,8 +6,7 @@ title: Home
 
 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.
+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>
 
@@ -28,7 +27,7 @@ incorporate.
 </div>
 
 !!! dna "Our Open Source Philosophy"
-    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)!
+    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_bioinformatics/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)! 
 
@@ -90,7 +89,7 @@ We would like to gratefully acknowledge the following individuals from the publi
 
 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](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.
+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 (now deprecated) 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](https://github.com/theiagen/public_health_bioinformatics/issues/new) or contact us at <[email protected]>.
 

docs/javascripts/table-search.js

@@ -0,0 +1,64 @@
+function addTableSearch() {
+    // Select all containers with the class 'searchable-table'
+    const containers = document.querySelectorAll('.searchable-table');
+
+    containers.forEach((container) => {
+        // Find the table within this container
+        const table = container.querySelector('table');
+
+        if (table) {
+            // Ensure we don't add multiple search boxes
+            if (!container.querySelector('input[type="search"]')) {
+                // Create the search input element
+                const searchInput = document.createElement("input");
+                searchInput.setAttribute("type", "search");
+                searchInput.setAttribute("placeholder", "Search table...");
+                searchInput.classList.add('table-search-input');
+                searchInput.style.marginBottom = "10px";
+                searchInput.style.display = "block";
+
+                // Insert the search input before the table
+                container.insertBefore(searchInput, container.firstChild);
+
+                // Add event listener for table search
+                searchInput.addEventListener("input", function () {
+                    const filter = searchInput.value.toUpperCase();
+                    const rows = table.getElementsByTagName("tr");
+
+                    for (let i = 1; i < rows.length; i++) { // Skip header row
+                        const cells = rows[i].getElementsByTagName("td");
+                        let match = false;
+
+                        for (let j = 0; j < cells.length; j++) {
+                            if (cells[j].innerText.toUpperCase().includes(filter)) {
+                                match = true;
+                                break;
+                            }
+                        }
+
+                        rows[i].style.display = match ? "" : "none";
+                    }
+                });
+            }
+        } else {
+            console.log('Table not found within container.');
+        }
+    });
+}
+
+// Run on page load
+addTableSearch();
+
+// Reapply search bar on page change
+function observeDOMChanges() {
+    const targetNode = document.querySelector('body');
+    const config = { childList: true, subtree: true };
+
+    const observer = new MutationObserver(() => {
+        addTableSearch();
+    });
+
+    observer.observe(targetNode, config);
+}
+
+observeDOMChanges();

docs/stylesheets/extra.css

@@ -184,5 +184,36 @@ th {
 td {
   word-break: break-all;
 }
+/* Base styles for the search box */
+div.searchable-table input.table-search-input {
+  width: 25%;
+  padding: 10px;
+  margin-bottom: 12px;
+  font-size: 12px;
+  box-sizing: border-box;
+  border-radius: 2px; 
+}
+
+/* Light mode styles */
+[data-md-color-scheme="light"] div.searchable-table input.table-search-input {
+  background-color: #fff;
+  color: #000;
+  border: 1px solid #E0E1E1;
+}
 
+[data-md-color-scheme="light"] div.searchable-table input.table-search-input::placeholder {
+  color: #888;
+  font-style: italic;
+}
 
+/* Dark mode styles */
+[data-md-color-scheme="slate"] div.searchable-table input.table-search-input {
+  background-color: #1d2125;
+  color: #fff;
+  border: 1px solid #373B40;
+}
+
+[data-md-color-scheme="slate"] div.searchable-table input.table-search-input::placeholder {
+  color: #bbb;
+  font-style: italic;
+}

docs/workflows/data_export/concatenate_column_content.md

@@ -16,6 +16,8 @@ This set-level workflow will create a file containing all of the items from a gi
 
 This workflow runs on the set level.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | concatenate_column_content | **concatenated_file_name** | String | The name of the output file. ***Include the extension***, such as ".fasta" or ".txt". |  | Required |
@@ -28,6 +30,8 @@ This workflow runs on the set level.
 | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
 | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 
+</div>
+
 ### Outputs
 
 !!! info

docs/workflows/data_export/transfer_column_content.md

@@ -25,6 +25,8 @@ This set-level workflow will transfer all of the items from a given column in a
 
 This workflow runs on the set level.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task name** | **input_variable** | **Type** | **Description** | **Default attribute** | **Status** |
 |---|---|---|---|---|---|
 | transfer_column_content | **files_to_transfer** | Array[File] | The column that has the files you want to concatenate. | | Required |
@@ -36,6 +38,8 @@ This workflow runs on the set level.
 | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
 | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 
+</div>
+
 ### Outputs
 
 !!! info

docs/workflows/data_export/zip_column_content.md

@@ -16,6 +16,8 @@ This workflow will create a zip file that contains all of the items in a column
 
 This workflow runs on the set level.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | zip_column_content | **files_to_zip** | Array[File] | The column that has the files you want to zip. |  | Required |
@@ -27,6 +29,8 @@ This workflow runs on the set level.
 | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
 | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 
+</div>
+
 ### Outputs
 
 !!! info

docs/workflows/data_import/assembly_fetch.md

@@ -23,6 +23,8 @@ Assembly_Fetch requires the input samplename, and either the accession for a ref
 
 This workflow runs on the sample level.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | reference_fetch | **samplename** | String | Your sample's name |  | Required |
@@ -44,6 +46,8 @@ This workflow runs on the sample level.
 | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
 | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 
+</div>
+
 ### Analysis Tasks
 
 ??? task "ReferenceSeeker (optional) Details"
@@ -90,6 +94,8 @@ This workflow runs on the sample level.
 
 ### Outputs
 
+<div class="searchable-table" markdown="1">
+
 | **Variable** | **Type** | **Description** |
 |---|---|---|
 | assembly_fetch_analysis_date | String | Date of assembly download |
@@ -101,11 +107,13 @@ This workflow runs on the sample level.
 | assembly_fetch_ncbi_datasets_version | String | NCBI datasets version used |
 | assembly_fetch_referenceseeker_database | String | ReferenceSeeker database used |
 | assembly_fetch_referenceseeker_docker | String | Docker file used for ReferenceSeeker |
-| assembly_fetch_referenceseeker_top_hit_ncbi_accession | String | NCBI Accession for the top it identified by Assembly_Fetch |
+| assembly_fetch_referenceseeker_top_hit_ncbi_accession | String | NCBI Accession for the top hit identified by Assembly_Fetch |
 | assembly_fetch_referenceseeker_tsv | File | TSV file of the top hits between the query genome and the Reference Seeker database |
 | assembly_fetch_referenceseeker_version | String | ReferenceSeeker version used |
 | assembly_fetch_version | String | The version of the repository the Assembly Fetch workflow is in |
 
+</div>
+
 ## References
 
 > **ReferenceSeeker:** Schwengers O, Hain T, Chakraborty T, Goesmann A. ReferenceSeeker: rapid determination of appropriate reference genomes. J Open Source Softw. 2020 Feb 4;5(46):1994.

docs/workflows/data_import/basespace_fetch.md

@@ -153,6 +153,8 @@ This process must be performed on a command-line (ideally on a Linux or MacOS co
 
 This workflow runs on the sample level.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | basespace_fetch | **access_token** | String | The access token is used in place of a username and password to allow the workflow to access the user account in BaseSpace from which the data is to be transferred. It is an alphanumeric string that is 32 characters in length. Example: 9e08a96471df44579b72abf277e113b7 | | Required |
@@ -168,6 +170,8 @@ This workflow runs on the sample level.
 | version_capture | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0" | Optional |
 | version_capture | **timezone** | String | Set the time zone to get an accurate date of analysis (uses UTC by default) |  | Optional |
 
+</div>
+
 ### **Outputs**
 
 The outputs of this workflow will be the fastq files imported from BaseSpace into the data table where the sample ID information had originally been uploaded.

docs/workflows/data_import/create_terra_table.md

@@ -19,6 +19,8 @@ The manual creation of Terra tables can be tedious and error-prone. This workflo
 
     **_This can be changed_** by providing information in the `file_ending` optional input parameter. See below for more information.
 
+<div class="searchable-table" markdown="1">
+
 | **Terra Task Name** | **Variable** | **Type** | **Description** | **Default Value** | **Terra Status** |
 |---|---|---|---|---|---|
 | create_terra_table | **assembly_data** | Boolean | Set to true if your data is in FASTA format; set to false if your data is FASTQ format | | Required |
@@ -33,6 +35,8 @@ The manual creation of Terra tables can be tedious and error-prone. This workflo
 | make_table | **docker** | String | The Docker container to use for the task | "us-docker.pkg.dev/general-theiagen/theiagen/terra-tools:2023-06-21" | Optional |
 | make_table | **memory** | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
 
+</div>
+
 ### Finding the `data_location_path`
 
 #### Using the Terra data uploader