add nf-test to CI

.github/workflows/ci.yml

@@ -4,43 +4,143 @@ on:
   push:
     branches:
       - dev
+      - master
   pull_request:
   release:
     types: [published]
 
 env:
   NXF_ANSI_LOG: false
-
+  NFTEST_VER: "0.8.1"
+# cancel if a newer run is started
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
-  test:
-    name: Run pipeline with test data
+  nftest-changes:
+    name: Check for changes (nf-test)
+    runs-on: ubuntu-latest
+    outputs:
+      tags: ${{ steps.filter.outputs.changes }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Combine all tags.yml files
+        id: get_tags
+        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
+
+      - name: debug
+        run: cat .github/tags.yml
+
+      - uses: frouioui/paths-filter@main
+        id: filter
+        with:
+          filters: ".github/tags.yml"
+          token: ""
+
+  nftest:
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/variantbenchmarking') }}"
+    if: needs.nftest-changes.outputs.tags != '[]'
     runs-on: ubuntu-latest
+    needs: nftest-changes
+
     strategy:
+      fail-fast: false
       matrix:
+        tags: ["${{ fromJson(needs.nftest-changes.outputs.tags) }}"]
+        profile: ["docker"]
+        # profile: ["docker", "singularity", "conda"]
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        include:
+          - tags: "pipeline_variantbenchmarking"
+            profile: "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
+      - uses: actions/setup-java@v3
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
+      - name: Conda setup
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run pipeline with test data for germline analysis
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Run nf-test
+        run: |
+          nf-test test tests/main.nf.test \
+            --profile=${{ matrix.profile }} \
+            --tag ${{ matrix.tags }} \
+            --tap=test.tap \
+            --verbose
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs:
+      - nftest
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        run: exit 0
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: debug-print
+        if: always()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          echo "toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"

.nf-core.yml

@@ -1,2 +1,4 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  actions_ci: false

tests/config/pytesttags.yaml

@@ -0,0 +1,4 @@
+# default
+default:
+  - "**"
+# default_extended

tests/main.nf.test

@@ -2,7 +2,8 @@ nextflow_pipeline {
 
     name "Test pipeline"
     script "../main.nf"
-    tag "PIPELINE"
+    tag "pipeline"
+    tag "pipeline_variantbenchmarking"
 
     test("Run with profile test") {
 
@@ -16,7 +17,7 @@ nextflow_pipeline {
                 outdir               = "$outputDir"
                 genome               = 'GRCh38'
                 analysis             = 'germline'
-                method               = 'happy,truvari,svanalyzer,wittyer,rtgtools'  //
+                method               = 'happy,truvari,svanalyzer,wittyer,rtgtools'
                 preprocess           = "normalization,deduplication,prepy"
                 sv_standardization   = "svync,homogenize"
                 include_expression   = 'FILTER="."'
@@ -29,6 +30,67 @@ nextflow_pipeline {
             }
         }
 
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+    test("Run with profile test somatic") {
+
+        when {
+            params {
+                max_cpus            = 2
+                max_memory          = '6.GB'
+                max_time            = '6.h'
+                input               = 'https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/sarek_full_test_somatic_v3.4.2/samplesheet_somatic.csv'
+                outdir              = 'results'
+                genome              = 'GRCh38'
+                analysis            = 'somatic'
+                sample              = "SEQC2"
+                method              = 'sompy,truvari'
+                preprocess          = "filter_contigs"
+                truth_snv           = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/sSNV_truth_set_v1.0.chr21.vcf.gz"
+                high_conf_snv       = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/high-confidence_sSNV_in_HC_regions_v1.2.chr21.vcf.gz"
+                truth_indel         = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/sINDEL_truth_set_v1.0.chr21.vcf.gz"
+                high_conf_indel     = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/high-confidence_sINDEL_in_HC_regions_v1.2.chr21.vcf.gz"
+                truth_sv            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/13059_2022_2816_MOESM4_ESM.vcf.gz"
+                itruth_ignore       = true
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+    test("Run with profile test liftover") {
+
+        when {
+            params {
+                    max_cpus            = 2
+                    max_memory          = '6.GB'
+                    max_time            = '6.h'
+                    input               = 'https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/samplesheet_HG002_hg38.csv'
+                    outdir              = 'results'
+                    genome              = 'GRCh38'
+                    analysis            = 'germline'
+                    sample              = "HG002"
+                    method              = 'truvari,svanalyzer,rtgtools,happy'
+                    preprocess          = "normalization,deduplication,filter_contigs"
+                    min_sv_size         = 30
+                    truth_small         = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_GRCh37_1_22_v4.2.1_highconf.chr21.vcf.gz"
+                    high_conf_small     = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_GRCh37_1_22_v4.2.1_highconf.bed"
+                    truth_sv            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_SVs_Tier1_v0.6.chr21.vcf.gz"
+                    high_conf_sv        = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/hg37/truth/HG002_SVs_Tier1_v0.6.chr21.bed"
+                    itruth_ignore       = true
+                    chain               = "https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/funcotator/data_sources/gnomAD/b37ToHg38.over.chain"
+                    rename_chr          = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt"
+                    liftover            = true
+                }
+            }
+
         then {
             assertAll(
                 { assert workflow.success }

tests/tags.yml

@@ -0,0 +1,5 @@
+pipeline_variantbenchmarking:
+  - "**.nf"
+  - "**.config"
+  - "**.nf.test"
+  - "**.json"