Updated tests and fusion containers and conda versions, general confi…

.github/workflows/ci.yml

@@ -5,11 +5,18 @@ on:
     branches:
       - dev
   pull_request:
+    branches:
+      - dev
+      - master
   release:
     types: [published]
   workflow_dispatch:
 
 env:
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -20,53 +27,54 @@ concurrency:
 
 jobs:
   test:
-    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
+    name: "${{ matrix.NXF_VER }} | ${{ matrix.test_profile }} | ${{ matrix.compute_profile }}"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnafusion') }}"
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "24.04.2"
           - "latest-stable"
-        trim_parameters:
-          - "--fastp_trim false"
-          - "--fastp_trim true"
-        profile:
-          - "conda"
+        test_profile:
+          - "test_stub"
+          - "test_build"
+        compute_profile:
           - "docker"
           - "singularity"
-        test_name:
-          - "test"
+          - "conda"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
         exclude:
           - isMaster: false
-            profile: "conda"
+            compute_profile: "conda"
           - isMaster: false
-            profile: "singularity"
+            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.profile == 'singularity'
+        if: matrix.compute_profile == 'singularity'
         uses: eWaterCycle/setup-apptainer@main
 
       - name: Set up Singularity
-        if: matrix.profile == 'singularity'
+        if: matrix.compute_profile == 'singularity'
         run: |
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
       - name: Set up Miniconda
-        if: matrix.profile == 'conda'
+        if: matrix.compute_profile == 'conda'
         uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:
           miniconda-version: "latest"
@@ -75,24 +83,40 @@ jobs:
           channels: conda-forge,bioconda
 
       - name: Set up Conda
-        if: matrix.profile == '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
 
-      - name: "Run pipeline build with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} \
-          -stub --build_references \
-          --outdir /home/runner/work/rnafusion/rnafusion/results --all \
-          --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \
-          --no_cosmic
+          python -m pip install --upgrade pip
+          pip install pdiff
+
+      - uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFT_VER }}
 
-      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+      - name: Run Tests (${{matrix.NXF_VER}} | ${{matrix.test_profile}} | ${{matrix.compute_profile}})
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} -stub \
-          --outdir /home/runner/work/rnafusion/rnafusion/results --all ${{ matrix.trim_parameters }} \
-          --genomes_base /home/runner/work/rnafusion/rnafusion/results/references
+          nf-test test \
+              --ci \
+              --tag ${{matrix.test_profile}} \
+              --profile "+${{ matrix.compute_profile }}" \
+              --junitxml=test.xml \
+              --debug --verbose
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml
+          annotate_only: true

CHANGELOG.md

@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add nf-test to local module: `ENSEMBL_DOWNLOAD` [#539](https://github.com/nf-core/rnafusion/pull/539)
 - Add nf-test to local module: `HGNC_DOWNLOAD` [#540](https://github.com/nf-core/rnafusion/pull/540)
 - Add nf-test to local subworkflow: `STRINGTIE_WORKFLOW` [#541](https://github.com/nf-core/rnafusion/pull/541)
-- Option to avoid using COSMIC (for example in the case of clinical use) [547](https://github.com/nf-core/rnafusion/pull/547)
+- Option to avoid using COSMIC (for example in the case of clinical use) [#547](https://github.com/nf-core/rnafusion/pull/547)
 - Add nf-test to nf-core module: `PICARD_COLLECTRNASEQMETRICS` and update module [#551](https://github.com/nf-core/rnafusion/pull/551)
 - Add `--skip_vcf` boolean parameter to skip vcf file generation [#554](https://github.com/nf-core/rnafusion/pull/554)
 - Add nf-test to local module: `FUSIONREPORT_DOWNLOAD` [#560](https://github.com/nf-core/rnafusion/pull/560)