Prepare artifacts

.github/scripts/install_conda.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 set -eo pipefail
 
-echo "Install Miniconda .." >> artifacts/test_artifact.log
+echo "Install Miniconda .." >> artifacts/test.log
 
 export PATH=/opt/miniconda3/bin:$PATH
 

.github/scripts/install_nextflow.sh

@@ -2,7 +2,7 @@
 
 set -eo pipefail
 
-echo Install Nextflow .. >> artifacts/test_artifact.log
+echo Install Nextflow .. >> artifacts/test.log
 
 wget -qO- https://get.nextflow.io | bash
 

.github/scripts/prepare_artifacts.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -eo pipefail
+
+echo "Prepare artifacts .." >> artifacts/test.log
+
+mkdir -p artifacts/fastq
+
+mv .github/data/fastq/*.fastq.gz artifacts/fastq
+

.github/workflows/pull_request.yml

@@ -32,6 +32,8 @@ jobs:
       run: bash .github/scripts/simulate_reads.sh
     - name: Run Pipeline
       run: bash .github/scripts/run_pipeline.sh
+    - name: Prepare Artifacts
+      run: bash .github/scripts/prepare_artifacts.sh
     - name: Upload Artifacts
       uses: actions/upload-artifact@v4
       if: always()