gzip reads and add pipeline run to workflow

BCCDC-PHL · Feb 8, 2024 · c63d251 · c63d251
1 parent 6358211
commit c63d251
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diff --git a/.github/scripts/simulate_reads.sh b/.github/scripts/simulate_reads.sh
@@ -20,3 +20,9 @@ art_illumina \
     --qShift 0 \
     --qShift2 0 \
     --out .github/data/fastq/NC000962.3_R
+
+mv .github/data/fastq/NC000962.3_R1.fq .github/data/fastq/NC000962.3_R1.fastq
+mv .github/data/fastq/NC000962.3_R2.fq .github/data/fastq/NC000962.3_R2.fastq
+
+gzip .github/data/fastq/NC000962.3_R1.fastq
+gzip .github/data/fastq/NC000962.3_R2.fastq
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -27,6 +27,8 @@ jobs:
       run: bash .github/scripts/download_assemblies.sh
     - name: Simulate Reads
       run: bash .github/scripts/simulate_reads.sh
+    - name: Run Pipeline
+      run: bash .github/scripts/run_pipeline.sh
     - name: Upload Artifacts
       uses: actions/upload-artifact@v4
       if: always()