From b6c0bdcf220f77cacd4f5f0917c57ce88c9bdea9 Mon Sep 17 00:00:00 2001
From: Dan Fornika <dfornika@gmail.com>
Date: Thu, 8 Feb 2024 15:33:18 -0800
Subject: [PATCH] Prepare artifacts

---
 .github/scripts/install_conda.sh     |  2 +-
 .github/scripts/install_nextflow.sh  |  2 +-
 .github/scripts/prepare_artifacts.sh | 10 ++++++++++
 .github/workflows/pull_request.yml   |  2 ++
 4 files changed, 14 insertions(+), 2 deletions(-)
 create mode 100755 .github/scripts/prepare_artifacts.sh

diff --git a/.github/scripts/install_conda.sh b/.github/scripts/install_conda.sh
index 5e38bf1..a31eb74 100755
--- a/.github/scripts/install_conda.sh
+++ b/.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
 
diff --git a/.github/scripts/install_nextflow.sh b/.github/scripts/install_nextflow.sh
index aeeff85..9819ed1 100755
--- a/.github/scripts/install_nextflow.sh
+++ b/.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
 
diff --git a/.github/scripts/prepare_artifacts.sh b/.github/scripts/prepare_artifacts.sh
new file mode 100755
index 0000000..7c774e0
--- /dev/null
+++ b/.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
+
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index f9fd56c..0c2a4b8 100644
--- a/.github/workflows/pull_request.yml
+++ b/.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()