Merge branch 'nf-test_implementation' into ci_test_branch_nf-core

.github/workflows/ci.yml

@@ -1,36 +1,82 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
   push:
     branches:
-      - dev
+      - "dev"
   pull_request:
+    branches:
+      - "dev"
+      - "master"
   release:
-    types: [published]
+    types:
+      - "published"
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.7.3"
 
 concurrency:
-  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: Run pipeline with assembly test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}"
+  define_nxf_versions:
+    name: Choose nextflow versions to test against depending on target branch
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.nxf_versions.outputs.matrix }}
+    steps:
+      - id: nxf_versions
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+          else
+            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
+          fi
+
+  test_profile_standard:
+    name: nf-test with standard profiles
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        tags:
+          - "test"
+          - "test_model_information"
+          - "test_mouse_all_pep_lengths"
+          - "test_assembly_only"
+          - "test_bins_only"
+          - "test_coassembly"
+          - "test_mhcflurry"
+          - "test_mhcnuggets_1"
+          - "test_mhcnuggets_2"
+        profile:
+          - "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
+      - name: Check out test data
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: metapep
+          path: test-datasets/
+          fetch-depth: 1
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheets/v1.0/*.csv; do
+            sed -i "s=https://github.com/nf-core/test-datasets/tree/metapep/testdata/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
         with:
@@ -39,63 +85,92 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-  profile:
-    name: Run additional profile tests
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        tests: [
-            "test_model_information",
-            "test_mouse_all_pep_lengths",
-            "test_assembly_only",
-            "test_bins_only",
-            "test_coassembly",
-            "test_mhcflurry",
-            "test_mhcnuggets_1",
-            "test_mhcnuggets_2",
-          ] # add further test profiles here, will be run in parallel (but only with one nextflow version)
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-      - name: Install Nextflow
+      - name: Run nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
 
-      - name: Run pipeline with profile ${{ matrix.tests }}
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker  --outdir ./results
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
 
-  all_profiles:
-    name: Run all additional profile tests that require ncbi credentials
-    # Only run on PRs from branches of nf-core/metapep repository or on push if this is the nf-core dev branch (merged PRs)
-    # (GitHub secrets are not accessible for workflows from forks)
-    if: ${{ github.event.pull_request.head.repo.full_name == 'nf-core/metapep' || (github.event_name == 'push' && github.repository == 'nf-core/metapep') }}
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "*.xml"
+
+  profile_download:
+    name: nf-test with profiles needing entrez downloads
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        tests: ["test_all", "test_mouse", "test_taxa_only", "test_taxa_specific_assembly"] # add further test profiles here, will be run in parallel (but only with one nextflow version)
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        tags:
+          - "test_all"
+          - "test_mouse"
+          - "test_taxa_only"
+          - "test_taxa_specific_assembly"
+        profile:
+          - "docker"
+
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+
+      - name: Check out test data
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: metapep
+          path: test-datasets/
+          fetch-depth: 1
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheets/v1.0/*.csv; do
+            sed -i "s=https://github.com/nf-core/test-datasets/tree/metapep/testdata/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
 
       - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - name: Install nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-      - name: Run pipeline with profile ${{ matrix.tests }}
+      - name: Run nf-test
         env:
           NCBI_EMAIL: ${{ secrets.NCBI_EMAIL }}
           NCBI_KEY: ${{ secrets.NCBI_KEY }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.tests }},docker --ncbi_email "$NCBI_EMAIL" --ncbi_key "$NCBI_KEY"  --outdir ./results
+          nf-test test --tag ${{ matrix.tags }} --profile ${{ matrix.tags }},${{ matrix.profile }} --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: "*.xml"

.gitignore

@@ -6,3 +6,6 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test/
+results_test/*
+.nf-test*

.nf-core.yml

@@ -1 +1,5 @@
 repository_type: pipeline
+lint:
+  files_exist:
+    - conf/igenomes.config
+  actions_ci: False

nf-test.config

@@ -0,0 +1,18 @@
+config {
+    // location for all nf-tests
+    testsDir "tests"
+
+    // nf-test directory including temporary files for each test
+    workDir ".nf-test"
+
+    // location of library folder that is added automatically to the classpath
+    libDir "tests/pipeline/lib/"
+
+    // location of an optional nextflow.config file specific for executing tests
+    configFile "tests/nextflow.config"
+
+    // run all test with the defined docker profile from the main nextflow.config
+    profile ""
+
+}
+

tests/nextflow.config

@@ -0,0 +1,4 @@
+env {
+    NCBI_EMAIL = "$NCBI_EMAIL"
+    NCBI_KEY   = "$NCBI_KEY"
+    }

tests/pipeline/test.nf.test

@@ -0,0 +1,22 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test"
+    tag "pipeline"
+
+    test("test assembly and bin input") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/pipeline/test_all.nf.test

@@ -0,0 +1,24 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_all"
+    tag "pipeline"
+
+    test("test all input path including protein downloads") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                ncbi_email = "\$NCBI_EMAIL"
+                ncbi_key = "\$NCBI_KEY"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/pipeline/test_assembly_only.nf.test

@@ -0,0 +1,22 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_assembly_only"
+    tag "pipeline"
+
+    test("test assembly input") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/pipeline/test_bins_only.nf.test

@@ -0,0 +1,22 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_bins_only"
+    tag "pipeline"
+
+    test("test bin input") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}

tests/pipeline/test_coassembly.nf.test

@@ -0,0 +1,22 @@
+nextflow_pipeline {
+
+    name "Test Workflow main.nf"
+    script "main.nf"
+    tag "test_coassembly"
+    tag "pipeline"
+
+    test("test coassembly input") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+
+    }
+
+}