update tests

.github/workflows/website.yml

@@ -34,21 +34,6 @@ jobs:
         env: 
           VITE_OFFLINE_VERSION: true
         run: npm run build
-      - name: Push offline mode to master
-        run: |  
-          git config --global user.name 'GitHub Actions'
-          git config --global user.email '[email protected]'
-          git add .
-
-          # Check for changes
-          if git diff-index --quiet HEAD --; then
-            # No changes
-            echo "No changes to commit"
-          else
-            # Changes detected
-            git commit -m "Add benchmarks / dist folder"
-            git push origin master
-          fi
       - name: Get installed Playwright version
         id: playwright-version
         run: echo "PLAYWRIGHT_VERSION=$(node -e "console.log(require('./package.json').devDependencies['@playwright/test'])")" >> $GITHUB_ENV
@@ -65,6 +50,21 @@ jobs:
         if: steps.playwright-cache.outputs.cache-hit == 'true'
       - name: Run Playwright deployment tests
         run: npx playwright test site-tests.spec.ts
+      - name: Push offline mode to master
+        run: |  
+          git config --global user.name 'GitHub Actions'
+          git config --global user.email '[email protected]'
+          git add .
+
+          # Check for changes
+          if git diff-index --quiet HEAD --; then
+            # No changes
+            echo "No changes to commit"
+          else
+            # Changes detected
+            git commit -m "Add benchmarks / dist folder"
+            git push origin master
+          fi
       - name: Build for github pages
         run: npm run build
       - name: Setup Pages

e2e/tests/download-benchmark-data.sh

@@ -25,6 +25,3 @@ seqtk sample -s100 reads.fastq.gz 10000 | gzip > reads_10k.fastq.gz
 
 # Subsample: 1k reads
 seqtk sample -s100 reads.fastq.gz 1000 | gzip > reads_1k.fastq.gz
-
-# Subsample: 100 reads
-seqtk sample -s100 reads.fastq.gz 100 | gzip > reads_100.fastq.gz

e2e/tests/run-baseline-benchmarks.sh

@@ -51,17 +51,6 @@ minimap2 -t 1 -a -o reads.sam NC_045512.2.fas reads_1k.fastq.gz
 grep "User time (seconds): " time_output.log | awk '{print $4}' >"$OUT_DIR/time.log"
 grep "Maximum resident set size (kbytes): " time_output.log | awk '{print $6}' >"$OUT_DIR/memory.log"
 
-### TEST #6: 100 reads.fastq.gz file (100 sequences)
-OUT_DIR=../../benchmarks/100/cli/
-mkdir -p $OUT_DIR
-
-minimap2 -t 1 -a -o reads.sam NC_045512.2.fas reads_100.fastq.gz
-/usr/bin/time -v viral_consensus -i reads.sam -r NC_045512.2.fas -o "$OUT_DIR/consensus.fa" -q 20 -d 10 -f 0.5 -a N 2>time_output.log
-
-grep "User time (seconds): " time_output.log | awk '{print $4}' >"$OUT_DIR/time.log"
-grep "Maximum resident set size (kbytes): " time_output.log | awk '{print $6}' >"$OUT_DIR/memory.log"
-
-
 
 rm reads.sam
 rm time_output.log

e2e/tests/site-benchmarks.spec.ts

@@ -11,12 +11,6 @@ const BENCHMARK_TESTS = {
 		outputFolder: 'example-uploaded/',
 		timeout: 10000
 	},
-	'100': {
-		alignmentFiles: ['./e2e/data/reads_100.fastq.gz'],
-		referenceFile: './e2e/data/NC_045512.2.fas',
-		outputFolder: '100/',
-		timeout: 10000
-	},
 	'1000': {
 		alignmentFiles: ['./e2e/data/reads_1k.fastq.gz'],
 		referenceFile: './e2e/data/NC_045512.2.fas',

src/App.jsx

@@ -804,7 +804,7 @@ export class App extends Component {
 								</div>
 							</div>
 
-							<h6 className="mt-5" id="additional-arguments" onClick={() => this.toggleAdditionalArgs()}>ViralConsensus Additional Arguments <i className={`bi bi-chevron-${this.state.tn93Open ? 'up' : 'down'}`}></i></h6>
+							<h6 className="mt-5" id="additional-arguments" onClick={() => this.toggleAdditionalArgs()}>ViralConsensus Additional Arguments <i className={`bi bi-chevron-${this.state.additionalArgsOpen ? 'up' : 'down'}`}></i></h6>
 							<hr></hr>
 
 							<div className={`${this.state.additionalArgsOpen ? '' : 'd-none'}`}>