nf-core · mashehu · May 27, 2025 · May 20, 2025 · May 20, 2025 · May 27, 2025
diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml
@@ -113,9 +113,6 @@ jobs:
       - name: run pipeline nf-test
         if: ${{ matrix.TEMPLATE  != 'all' && matrix.TEMPLATE != 'nf-test' }}
         shell: bash
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
           cd create-test-lint-wf/my-prefix-testpipeline
           nf-test test \

diff --git a/.github/workflows/create-test-wf.yml b/.github/workflows/create-test-wf.yml
@@ -77,9 +77,6 @@ jobs:
 
       - name: Run nf-test
         shell: bash
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
         run: |
           cd create-test-wf/nf-core-testpipeline
           nf-test test \

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -83,6 +83,7 @@
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.9 ([#3563](https://github.com/nf-core/tools/pull/3563))
 - chore(deps): update python:3.12-slim docker digest to 31a416d ([#3568](https://github.com/nf-core/tools/pull/3568))
 - chore(deps): update codecov/codecov-action digest to 18283e0 ([#3575](https://github.com/nf-core/tools/pull/3575))
+- use pdiff from setup-nf-test ([#3578](https://github.com/nf-core/tools/pull/3578))
 - chore(deps): update python:3.12-slim docker digest to fd95fa2 ([#3587](https://github.com/nf-core/tools/pull/3587))
 - chore(deps): update gitpod/workspace-base docker digest to 3aa18f4 ([#3586](https://github.com/nf-core/tools/pull/3586))
 - chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.11.11 ([#3585](https://github.com/nf-core/tools/pull/3585))

diff --git a/nf_core/pipeline-template/.github/actions/nf-test/action.yml b/nf_core/pipeline-template/.github/actions/nf-test/action.yml
@@ -33,6 +33,7 @@ runs:
       uses: nf-core/setup-nf-test@v1
       with:
         version: "${{ env.NFT_VER }}"
+        install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
@@ -53,11 +54,6 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-    - name: Install pdiff
-      shell: bash
-      run: |
-        python -m pip install pdiff
-
       # TODO Skip failing conda tests and document their failures
       # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test

diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -25,8 +25,6 @@ concurrency:
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_DIFF: "pdiff"
-  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
   NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false