use pdiff installed and setup by setup-nf-test

Author: mashehu

.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 \

.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 \

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

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