diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml index c96463c..3a4b9cf 100644 --- a/.github/workflows/website.yml +++ b/.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 'action@github.com' - 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 'action@github.com' + 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 diff --git a/e2e/tests/download-benchmark-data.sh b/e2e/tests/download-benchmark-data.sh index 7e83c31..e2ed4ad 100644 --- a/e2e/tests/download-benchmark-data.sh +++ b/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 diff --git a/e2e/tests/run-baseline-benchmarks.sh b/e2e/tests/run-baseline-benchmarks.sh index 2d5de6c..b081b6c 100644 --- a/e2e/tests/run-baseline-benchmarks.sh +++ b/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 \ No newline at end of file diff --git a/e2e/tests/site-benchmarks.spec.ts b/e2e/tests/site-benchmarks.spec.ts index e50db33..09e3426 100644 --- a/e2e/tests/site-benchmarks.spec.ts +++ b/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', diff --git a/src/App.jsx b/src/App.jsx index a7f5ab6..91ebd6a 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -804,7 +804,7 @@ export class App extends Component { -
this.toggleAdditionalArgs()}>ViralConsensus Additional Arguments
+
this.toggleAdditionalArgs()}>ViralConsensus Additional Arguments