From e35d04f94efc7e282dcc17eefb094fb623b3b796 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Thu, 9 Jan 2025 10:38:50 +0100
Subject: [PATCH 1/4] Test fix for downloading

---
 .github/workflows/download_pipeline.yml | 36 ++++++++++++++-----------
 CHANGELOG.md                            |  4 +--
 2 files changed, 22 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 13b51e2c..2b85306e 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 %}{% if test_config %}{% raw %}
+
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - 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 29ffb267..c4b443db 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,12 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.2.2 - Bouncy Basenji Patch [2024-12-20]
+## v1.2.2 - Bouncy Basenji Patch [2024-01-13]
 
 ### `Added`
 
 - [#558](https://github.com/nf-core/taxprofiler/pull/558) Updated to nf-core pipeline template v3.1.0 (added by @LilyAnderssonLee)
-- [#565](https://github.com/nf-core/taxprofiler/pull/565) Update to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)
+- [#565](https://github.com/nf-core/taxprofiler/pull/565) Updated to nf-core pipeline template v3.1.1 (added by @LilyAnderssonLee)
 
 ### `Fixed`
 

From e34c7a4875bccb9c7af31c53b5b1d93540aa28d4 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Thu, 9 Jan 2025 11:35:12 +0100
Subject: [PATCH 2/4] Check if the fix works when opening PR against dev

---
 .github/workflows/download_pipeline.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2b85306e..e937931f 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -19,6 +19,7 @@ on:
     branches:
       - main
       - master
+      - dev
   pull_request_target:
     branches:
       - main

From a22afb218d6d7628bae03f9c5ab52542fa609875 Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Thu, 9 Jan 2025 12:56:22 +0100
Subject: [PATCH 3/4] Remove the dev from branches

---
 .github/workflows/download_pipeline.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index e937931f..2b85306e 100644
--- a/.github/workflows/download_pipeline.yml
+++ b/.github/workflows/download_pipeline.yml
@@ -19,7 +19,6 @@ on:
     branches:
       - main
       - master
-      - dev
   pull_request_target:
     branches:
       - main

From 6843bdf396d7e822b6a3f20fa3f62b05e741c09c Mon Sep 17 00:00:00 2001
From: sofstam <sofia.stamouli@scilifelab.se>
Date: Thu, 9 Jan 2025 14:17:42 +0100
Subject: [PATCH 4/4] Test new fix

---
 .github/workflows/download_pipeline.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
index 2b85306e..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 }} \
@@ -85,7 +85,7 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
       - name: Inspect container images
         run: tree ./singularity_container_images | tee ./container_initial
@@ -131,4 +131,4 @@ jobs:
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"
-          fi{% endraw %}{% endif %}
+          fi