Merge pull request #2642 from mashehu/add-pdiff-to-docker-image

Set pdiff as nf-test differ in Docker image for Gitpod
nf-core · Jan 8, 2024 · 501b6f0 · 501b6f0
2 parents 97e9bd4 + 22613c5
commit 501b6f0
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Showing 4 changed files with 7 additions and 11 deletions.
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -10,11 +10,6 @@ tasks:
     command: |
       unset JAVA_TOOL_OPTIONS
 
-  - name: Use pdiff for nf-test diff viewing
-    command: |
-      export NFT_DIFF="pdiff"
-      export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
-
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,6 @@
 ### Template
 
 - Use `pre-commit` to lint files in GitHub CI ([#2635](https://github.com/nf-core/tools/pull/2635))
-- Use pdiff also on gitpod for nf-test ([#2640](https://github.com/nf-core/tools/pull/2640))
 
 ### Download
 
@@ -22,6 +21,7 @@
 - Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 ([#2630](https://github.com/nf-core/tools/pull/2630))
 - Update mshick/add-pr-comment action to v2 ([#2632](https://github.com/nf-core/tools/pull/2632))
 - update python image version in docker file ([#2636](https://github.com/nf-core/tools/pull/2636))
+- Set pdiff as nf-test differ in Docker image for Gitpod ([#2642](https://github.com/nf-core/tools/pull/2642))
 
 # [v2.11.1 - Magnesium Dragon Patch](https://github.com/nf-core/tools/releases/tag/2.11) - [2023-12-20]
 

diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile
@@ -62,4 +62,8 @@ RUN conda config --add channels defaults && \
 RUN nextflow self-update
 
 # Install nf-core
-RUN python -m pip install .
+RUN python -m pip install . --no-cache-dir
+
+# Setup pdiff for nf-test diffs
+RUN export NFT_DIFF="pdiff" && \
+    export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml
@@ -7,10 +7,7 @@ tasks:
   - name: unset JAVA_TOOL_OPTIONS
     command: |
       unset JAVA_TOOL_OPTIONS
-  - name: Use pdiff for nf-test diff viewing
-    command: |
-      export NFT_DIFF="pdiff"
-      export NFT_DIFF_ARGS="--line-numbers --expand-tabs=2"
+
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files