chore(dev): skip missing remap vircov pd

app/src/lib/components/data/sample/cards/InternalControls.svelte

@@ -1,4 +1,5 @@
 <script lang="ts">
+    import '@carbon/charts-svelte/styles.css'
 	import { BarChartSimple, ChartTheme, ScaleTypes } from '@carbon/charts-svelte';
 	import type { OrganismControl, Cerebro } from '$lib/utils/types';
 
@@ -59,6 +60,7 @@
 		grid: {
 			y: { enabled: false },
 			x: { enabled: false },
+			backgroundColor: "transparent"
 		},
 		axes: {
 			left: {
@@ -92,7 +94,11 @@
     <p class="text-xs opacity-60 flex justify-start pb-8">
         <span>Internal control coverage</span>
     </p>
-        <BarChartSimple data={organismControlData} options={barChartOptions} />
+
+	<div class="qc-internal-controls">
+    	<BarChartSimple data={organismControlData} options={barChartOptions} />
+	</div>
+
     {:else}
         <div class="flex justify-center">
             <p class="text-sm opacity-60 pt-24">No organism control data available</p>
@@ -101,17 +107,9 @@
 </div>
 
 
-<!-- 
-Overwrite the root variable that is responsible
-for setting the background colors of the Carbon  
-plot - there is probably a way to adjust these 
-to the Skeleton UI / Tailwind color scheme 
-variables but it is eluding me...
--->
 <style lang="postcss">
-    :root {
-         --cds-grid-bg: rgb(0, 0, 0, 0);
+	/* Scoped globally but applied only within this component */
+    :global(.qc-internal-controls .chart-grid-backdrop) {
+        display: none;
     }
-</style>
-
-<link rel="stylesheet" href="/carbon.css">
+</style>

app/src/lib/components/data/sample/cards/ReadQuality.svelte

@@ -1,4 +1,5 @@
 <script lang="ts">
+    import '@carbon/charts-svelte/styles.css'
     import { MeterChart, ChartTheme } from '@carbon/charts-svelte'
     import { Statuses } from '@carbon/charts';
 	import { type Cerebro } from '$lib/utils/types';
@@ -220,24 +221,17 @@
 </div>
 
 <style lang="postcss">
-    :root {
-         --cds-grid-bg: rgba(0, 0, 0, 0);
-    }
-    .qc-meter-chart {
-        --cds-grid-bg: rgba(0, 0, 0, 0.1); /* Set desired background */
-    }
     /* Scoped globally but applied only within this component */
-    :global(.proportional-meter-total) {
+    :global(.qc-meter-chart .proportional-meter-total) {
         display: none;
     }
     /* Scoped globally but applied only within this component */
-    :global(.proportional-meter-title) {
+    :global(.qc-meter-chart .proportional-meter-title) {
         display: none;
     }
     /* Scoped globally but applied only within this component */
-    :global(.status-indicator) {
+    :global(.qc-meter-chart .status-indicator) {
         display: none;
     }
 </style>
-
-<link rel="stylesheet" href="/carbon.css">
+

app/src/lib/components/data/sample/cards/SyntheticControls.svelte

@@ -1,4 +1,5 @@
 <script lang="ts">
+    import '@carbon/charts-svelte/styles.css'
 	import { ERCC_CONCENTRATIONS, ERCC_GROUPS, getCssVariableAsHex } from "$lib/utils/helpers";
 	import type { Cerebro, ErccControl } from "$lib/utils/types";
 	import { sampleCorrelation } from "simple-statistics";
@@ -156,7 +157,9 @@
             <span class="ml-5 text-xs opacity-40">r<sup>2</sup><sub>C</sub> = {groupCoefficients.C.toFixed(4)}</span>
             <span class="ml-5 text-xs opacity-40">r<sup>2</sup><sub>D</sub> = {groupCoefficients.D.toFixed(4)}</span>
         </p>
-        <ScatterChart data={correlationData} options={correlationPlotOptions}></ScatterChart>
+        <div class="qc-ercc-chart">
+            <ScatterChart data={correlationData} options={correlationPlotOptions}></ScatterChart>
+        </div>
 
     {:else}
         <div class="flex justify-center">
@@ -168,15 +171,10 @@
 
 </div>
 
-<!-- 
-Overwrite the root variable that is responsible
-for setting the background colors of the Carbon  
-plot - there is probably a way to adjust these 
-to the Skeleton UI / Tailwind color scheme 
-variables but it is eluding me...
--->
+
 <style lang="postcss">
-   :root {
-        --cds-grid-bg: rgb(0, 0, 0, 0);
-   }
+	/* Scoped globally but applied only within this component */
+    :global(.qc-ercc-chart .chart-grid-backdrop) {
+        display: none;
+    }
 </style>

app/src/lib/components/visualisations/taxa/heatmap/TaxonHeatmap.svelte

@@ -295,12 +295,13 @@
         <label class="label">
             <span class="font-medium mb-2">Read classifier</span>
             <select bind:value={tool} class="select">
-                <option value="{PathogenDetectionTool.Ganon2}">{PathogenDetectionTool.Ganon2}</option>
                 <option value="{PathogenDetectionTool.Kraken2}">{PathogenDetectionTool.Kraken2}</option>
+                <option value="{PathogenDetectionTool.Ganon2}">{PathogenDetectionTool.Ganon2}</option>
                 <option value="{PathogenDetectionTool.Bracken}">{PathogenDetectionTool.Bracken}</option>
                 <option value="{PathogenDetectionTool.Metabuli}">{PathogenDetectionTool.Metabuli}</option>
                 <option value="{PathogenDetectionTool.Kmcp}">{PathogenDetectionTool.Kmcp}</option>
                 <option value="{PathogenDetectionTool.Sylph}">{PathogenDetectionTool.Sylph}</option>
+                <option value="{PathogenDetectionTool.Vircov}">{PathogenDetectionTool.Vircov}</option>
             </select>
         </label>
 

cerebro/stack/client/src/cli.rs

@@ -12,8 +12,8 @@ use cerebro_client::utils::init_logger;
 use cerebro_client::client::CerebroClient;
 use cerebro_client::terminal::{TowerCommands, ProjectCommands, StageCommands, WatcherCommands, App, Commands};
 
-// use cerebro_pipe::sample::WorkflowSample;
 use cerebro_model::api::cerebro::model::Cerebro;
+use cerebro_pipe::taxa::taxon::TaxonExtraction;
 
 fn main() -> anyhow::Result<()> {
 

cerebro/stack/pipe/src/modules/panviral.rs

@@ -4,7 +4,7 @@ use serde::{Deserialize, Serialize};
 use taxonomy::ncbi;
 use vircov::vircov::VircovRecord;
 
-use crate::{error::WorkflowError, nextflow::panviral::PanviralOutput, taxa::taxon::Taxon, utils::read_tsv};
+use crate::{error::WorkflowError, nextflow::panviral::PanviralOutput, taxa::taxon::{Taxon, TaxonExtraction}, utils::read_tsv};
 
 use super::quality::QualityControl;
 
@@ -46,36 +46,45 @@ impl Panviral {
         let pathogen = serde_json::from_reader(reader)?;
         Ok(pathogen)
     }
-    // Uses the provided taxonomy to create the taxon structs for the database model
-    pub fn get_taxa(&self, taxonomy_directory: &PathBuf, strict: bool) -> Result<HashMap<String, Taxon>, WorkflowError> {
+}
 
+impl TaxonExtraction for Panviral {
+    fn get_taxa(&self, taxonomy_directory: &PathBuf, strict: bool) -> Result<HashMap<String, Taxon>, WorkflowError> {
         let taxonomy = ncbi::load(taxonomy_directory)?;
-
-        let mut taxa = HashMap::new();
+    
+        let mut taxa: HashMap<String, Taxon> = HashMap::new();
         for record in &self.records {
-
             let taxid = match &record.taxid {
                 None => {
                     log::error!("Taxid not found for record with reference sequence: {}", record.reference);
-                    return Err(WorkflowError::PanviralTaxidAnnotationMissing)
-                },
-                Some(taxid) => taxid
-            };
-
-            let mut taxon = match Taxon::from_taxid(taxid.clone(), &taxonomy, true) {
-                Err(err) => {
-                    log::error!("Failed to find taxid '{}' in provided taxonomy", taxid);
-                    if strict {
-                        return Err(err)
-                    } else {
-                        log::warn!("Strict mode is not enabled - detection of taxid '{}' will be skipped", taxid);
-                        continue;
-                    }
+                    return Err(WorkflowError::PanviralTaxidAnnotationMissing);
                 },
-                Ok(taxon) => taxon,
+                Some(taxid) => taxid,
             };
-            taxon.evidence.alignment.push(record.clone());
-            taxa.insert(taxid.clone(), taxon);
+
+            if let Some(existing_taxon) = taxa.get_mut(taxid) {
+                // If the taxid is already present, update its evidence
+                existing_taxon.evidence.alignment.push(record.clone());
+            } else {
+                // Otherwise, create a new Taxon and insert it into the HashMap
+                let mut taxon = match Taxon::from_taxid(taxid.clone(), &taxonomy, true) {
+                    Err(err) => {
+                        log::error!("Failed to find taxid '{}' in provided taxonomy", taxid);
+                        if strict {
+                            return Err(err);
+                        } else {
+                            log::warn!(
+                                "Strict mode is not enabled - detection of taxid '{}' will be skipped",
+                                taxid
+                            );
+                            continue;
+                        }
+                    },
+                    Ok(taxon) => taxon,
+                };
+                taxon.evidence.alignment.push(record.clone());
+                taxa.insert(taxid.clone(), taxon);
+            }
         }
         Ok(taxa)
     }

cerebro/stack/pipe/src/modules/pathogen.rs

@@ -3,7 +3,7 @@ use std::{collections::HashMap, fs::File, io::{BufReader, BufWriter}, path::{Pat
 use serde::{Deserialize, Serialize};
 use taxonomy::{ncbi, GeneralTaxonomy, TaxRank, Taxonomy};
 
-use crate::{error::WorkflowError, nextflow::pathogen::{PathogenOutput, SylphReportRecord}, taxa::taxon::Taxon, utils::{read_tsv, write_tsv}};
+use crate::{error::WorkflowError, nextflow::pathogen::{PathogenOutput, SylphReportRecord}, taxa::taxon::{Taxon, TaxonExtraction}, utils::{read_tsv, write_tsv}};
 
 use super::quality::QualityControl;
 
@@ -273,7 +273,7 @@ impl PathogenDetection {
 
                 let remap_reads = match record.remap_alignments {
                     Some(reads) => reads,
-                    None => return Err(WorkflowError::PathogenRemapDataMissing)
+                    None => continue // remapping stage unsuccessful - can occur when very few reads detectec in scanning stage
                 };
 
 
@@ -543,34 +543,6 @@ impl PathogenDetection {
             .cloned()
             .collect()
     }
-    // Uses the provided taxonomy to create the taxon structs for the database model
-    pub fn get_taxa(&self, taxonomy_directory: &PathBuf, strict: bool) -> Result<HashMap<String, Taxon>, WorkflowError> {
-
-        let taxonomy = ncbi::load(taxonomy_directory)?;
-
-        let mut taxa = HashMap::new();
-
-        // Pathogen detection records
-        for record in &self.records {
-
-            let mut taxon = match Taxon::from_taxid(record.taxid.clone(), &taxonomy, true) {
-                Ok(taxon) => taxon,
-                Err(err) => {
-                    log::error!("Failed to find taxid '{}' in provided taxonomy", record.taxid);
-                    if strict {
-                        return Err(err)
-                    } else {
-                        log::warn!("Strict mode is not enabled - detection of taxid '{}' will be skipped", record.taxid);
-                        continue;
-                    }
-                }
-            };
-            taxon.evidence.records.push(record.clone());
-            taxa.insert(record.taxid.clone(), taxon);
-        }
-
-        Ok(taxa)
-    }
     pub fn write_records(records: &Vec<PathogenDetectionRecord>, path: &Path) -> Result<(), WorkflowError> {
         write_tsv(&records, path, true)
     }
@@ -599,6 +571,41 @@ impl PathogenDetection {
     }
 }
 
+impl TaxonExtraction for PathogenDetection {
+    fn get_taxa(&self, taxonomy_directory: &PathBuf, strict: bool) -> Result<HashMap<String, Taxon>, WorkflowError> {
+        let taxonomy = ncbi::load(taxonomy_directory)?;
+
+        let mut taxa: HashMap<String, Taxon> = HashMap::new();
+        for record in &self.records {
+
+            if let Some(existing_taxon) = taxa.get_mut(&record.taxid) {
+                // If the taxid is already present, update its evidence
+                existing_taxon.evidence.records.push(record.clone());
+            } else {
+                // Otherwise, create a new Taxon and insert it into the HashMap
+                let mut taxon = match Taxon::from_taxid(record.taxid.clone(), &taxonomy, true) {
+                    Err(err) => {
+                        log::error!("Failed to find taxid '{}' in provided taxonomy", &record.taxid);
+                        if strict {
+                            return Err(err);
+                        } else {
+                            log::warn!(
+                                "Strict mode is not enabled - detection of taxid '{}' will be skipped",
+                                record.taxid
+                            );
+                            continue;
+                        }
+                    },
+                    Ok(taxon) => taxon,
+                };
+                taxon.evidence.records.push(record.clone());
+                taxa.insert(record.taxid.clone(), taxon);
+            }
+        }
+        Ok(taxa)
+    }
+}
+
 #[derive(Debug, Clone, Serialize, Deserialize, PartialEq, clap::ValueEnum)]
 pub enum PathogenDetectionRank {
     Superkingdom,

cerebro/stack/pipe/src/taxa/taxon.rs

@@ -11,6 +11,10 @@ use crate::modules::pathogen::{PathogenDetectionRecord, PathogenDetectionResult}
 use crate::{error::WorkflowError, utils::get_colored_string};
 
 
+pub trait TaxonExtraction {
+    fn get_taxa(&self, taxonomy_directory: &PathBuf, strict: bool) -> Result<HashMap<String, Taxon>, WorkflowError>;
+}
+
 fn _get_annotations(taxon: &Taxon, annotations: &Vec<TaxonAnnotations>) -> Option<String> {
 
     let annotation_strings: Vec<String> = annotations.iter().map(|data| {

lib/production/utils.nf

@@ -13,10 +13,12 @@ def getProductionConfig() {
 /* Panviral Enrichment */
 
 def getPanviralEnrichmentDatabases() {
+
     return [
         panviralEnrichment: getPanviralEnrichmentVirusDatabases(),
         qualityControl: getQualityControlDatabases(),
     ]
+
 }
 
 def getPanviralEnrichmentVirusDatabases() {
@@ -43,6 +45,7 @@ def getPanviralEnrichmentTaxonomy() {
 /* Pathogen Detection */
 
 def getPathogenDetectionDatabases() {
+
     return [
         qualityControl: getQualityControlDatabases(),
         taxonomicProfile: getTaxonomicProfileDatabases(),
@@ -67,8 +70,6 @@ def getMetagenomeAssemblyDatabases() {
 
     def magParams = params.pathogenDetection.metagenomeAssembly;
 
-    log.info "$params"
-
     return [
         ncbiDatabase:       magParams.ncbiDatabase    ?  getPathogenAssemblyNcbiDatabase(magParams)          :  Channel.empty(),
         sylphDatabase:      magParams.contigProfile   ?  getPathogenAssemblySylphDatabase(magParams)         :  Channel.empty(),