Fixed test profiles

.github/workflows/ci.yml

@@ -1,5 +1,5 @@
 name: nf-core CI
-
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
   push:
     branches:
@@ -26,9 +26,10 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  test_with_test_profile:
+  test:
     name: "${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }}"
-    if: github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion')
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion') }}"
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -40,11 +41,12 @@ jobs:
           - "test_stub"
           - "test_build_stub"
         compute_profile:
-          - "conda"
           - "docker"
           - "singularity"
+          - "conda"
         isMaster:
           - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
         exclude:
           - isMaster: false
             compute_profile: "conda"
@@ -114,101 +116,7 @@ jobs:
 
       - name: Publish Test Report
         uses: mikepenz/action-junit-report@v3
-        if: always()
-        with:
-          report_paths: test.xml
-          annotate_only: true
-
-  test_with_secret_test_profile:
-    name: "${{ matrix.NXF_VER }} | ${{ matrix.secret_test_profile }} | ${{ matrix.compute_profile }}"
-    if: github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion')
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
-        secret_test_profile:
-          - "test"
-          - "test_build"
-          - "test_cosmic"
-        compute_profile:
-          - "conda"
-          - "docker"
-          - "singularity"
-        isMaster:
-          - ${{ github.base_ref == 'master' }}
-        exclude:
-          - isMaster: false
-            compute_profile: "conda"
-          - isMaster: false
-            compute_profile: "singularity"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Apptainer
-        if: matrix.compute_profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.compute_profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Miniconda
-        if: matrix.compute_profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          conda-solver: libmamba
-          channels: conda-forge,bioconda
-
-      - name: Set up Conda
-        if: matrix.compute_profile == 'conda'
-        run: |
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
-      - name: Install pdiff to see diff between nf-test snapshots
-        run: |
-          python -m pip install --upgrade pip
-          pip install pdiff
-
-      - uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFT_VER }}
-
-      - name: Run Tests (${{matrix.NXF_VER}} | ${{matrix.secret_test_profile}} | ${{matrix.compute_profile}})
-        run: |
-          nf-test test \
-              --ci \
-              --tag ${{matrix.secret_test_profile}} \
-              --profile "+${{ matrix.compute_profile }}" \
-              --junitxml=test.xml \
-              --debug --verbose
-
-      - name: Publish Test Report
-        uses: mikepenz/action-junit-report@v3
-        if: always()
+        if: always() # always run even if the previous step fails
         with:
           report_paths: test.xml
           annotate_only: true

nextflow.config

@@ -228,9 +228,6 @@ profiles {
     test_cosmic {
         includeConfig 'conf/test_cosmic.config'
     }
-    test_full {
-        includeConfig 'conf/test_full.config'
-    }
 
     gitpod {
         executor.name           = 'local'

tests/test.nf.test

@@ -48,8 +48,23 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
-                { assert workflow.success }
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }

tests/test_build.nf.test

@@ -5,7 +5,7 @@ nextflow_pipeline {
     profile "test_build"
     tag "pipeline"
     tag "pipeline_rnafusion"
-    tag "build"
+    tag "test_build"
 
     test("test_build with fastp_trim") {
 
@@ -48,8 +48,23 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
-                { assert workflow.success }
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }

tests/test_build_stub.nf.test

@@ -6,7 +6,7 @@ nextflow_pipeline {
     options "-stub" // TODO remove once the pipeline is fixed
     tag "pipeline"
     tag "pipeline_rnafusion"
-    tag "build"
+    tag "test_build_stub"
 
     test("stub test_build with fastp_trim") {
 

tests/test_cosmic.nf.test

@@ -48,8 +48,54 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("test cosmic no fastp trim build") {
+
+        when {
+            params {
+                outdir     = "$outputDir"
+                fastp_trim = false
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
-                { assert workflow.success }
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }

tests/test_stub.nf.test

@@ -6,7 +6,7 @@ nextflow_pipeline {
     options "-stub" // TODO remove once the pipeline is fixed
     tag "pipeline"
     tag "pipeline_rnafusion"
-    tag "test"
+    tag "test_stub"
 
     test("stub test with fastp trim") {
 
@@ -55,8 +55,23 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            // Ignore files with timestamps in their names
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
-                { assert workflow.success }
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }