From 5d325a4079b77fcf0e90a3a968f6b13964710d96 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 20 Jan 2025 08:51:17 +0100
Subject: [PATCH 1/2] Fix download tests

---
 .github/workflows/download_pipeline.yml | 36 ++++++++++++++-----------
 CHANGELOG.md                            |  1 +
 2 files changed, 21 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 13b51e2c..977b4255 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -29,11 +29,22 @@ env:
 
 jobs:
   configure:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-latest{% raw %}
     outputs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -56,24 +67,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        id: get_repo_properties
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
-  download:
-    runs-on: ubuntu-latest
-    needs: configure
-    steps:
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %}
         run: |
           nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
           --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
@@ -85,7 +85,10 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %}
 
       - name: Count the downloaded number of container images
         id: count_initial
@@ -123,8 +126,9 @@ jobs:
             final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
-          fi
+          fi{% endraw %}{% endif %}
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ce4f6e9b..a84aa7fa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- Download tests [#667](https://github.com/nf-core/raredisease/pull/667)
 - Restrict deepvariant analysis of WES samples to bait regions [#633](https://github.com/nf-core/raredisease/pull/633), [#658](https://github.com/nf-core/raredisease/pull/658)
 - bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
 - Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)

From a76c9bae22131231a84d188e61053ae3c45350a7 Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Mon, 20 Jan 2025 11:35:32 +0100
Subject: [PATCH 2/2] remove template

---
 .github/workflows/download_pipeline.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 977b4255..ab06316e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -29,7 +29,7 @@ env:
 
 jobs:
   configure:
-    runs-on: ubuntu-latest{% raw %}
+    runs-on: ubuntu-latest
     outputs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
@@ -40,7 +40,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest
@@ -73,7 +73,7 @@ jobs:
 
       - name: Download the pipeline
         env:
-          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %}
+          NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
           nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
           --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
@@ -85,10 +85,10 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
       - name: Inspect container images
-        run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %}
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial
@@ -131,4 +131,4 @@ jobs:
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
-          fi{% endraw %}{% endif %}
+          fi