add nf-test to CI

.github/include.yaml

@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

.github/workflows/ci.yml

@@ -4,28 +4,66 @@ on:
   push:
     branches:
       - dev
+      - master
   pull_request:
   release:
     types: [published]
 
 env:
   NXF_ANSI_LOG: false
-
+  NFTEST_VER: "0.9"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+# 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:
+      nf_test_files: ${{ steps.list.outputs.components }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.2
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
+
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
+  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.nf_test_files != '[]'
     runs-on: ubuntu-latest
+    needs: [nftest-changes]
+
     strategy:
+      fail-fast: false
       matrix:
+        profile:
+          - "docker"
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        nf_test_files: ["${{ fromJson(needs.nftest-changes.outputs.nf_test_files) }}"]
+        include:
+          - tags: "pipeline_variantbenchmarking"
+            profile: "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -35,12 +73,54 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        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
+
+      - name: Run nf-test
+        run: |
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - 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
+
+  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: 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: 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

conf/modules.config

@@ -24,6 +24,7 @@ process {
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
+        container = "community.wave.seqera.io/library/multiqc:1.22.1--4886de6095538010"
     }
     // standardization and normalization tools
     withName: "BCFTOOLS_NORM" {

conf/test_liftover.config

@@ -39,6 +39,6 @@ params {
 
     //liftover files
     chain                = "https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/funcotator/data_sources/gnomAD/b37ToHg38.over.chain"
-    rename_chr           = "assets/rename_contigs/grch37_grch38.txt"
+    rename_chr           = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt"
     liftover             = true
 }

conf/truth.config

@@ -18,7 +18,7 @@ params {
                 truth_sv              = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.vcf.gz"
                 high_conf_sv          = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/CMRG_v1.00/GRCh38/StructuralVariant/HG002_GRCh38_CMRG_SV_v1.00.bed"
                 chain                 = "http://ftp.ensembl.org/pub/assembly_mapping/homo_sapiens/GRCh38_to_GRCh37.chain.gz"
-                rename_chr            = "assets/rename_contigs/grch38_grch37.txt"
+                rename_chr            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch38_grch37.txt"
             }
         }
         'GRCh37'{
@@ -28,7 +28,7 @@ params {
                 truth_sv              = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NIST_SV_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz"
                 high_conf_sv          = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NIST_SV_v0.6/HG002_SVs_Tier1_v0.6.bed"
                 chain                 = "https://raw.githubusercontent.com/broadinstitute/gatk/master/scripts/funcotator/data_sources/gnomAD/b37ToHg38.over.chain"
-                rename_chr            = "assets/rename_contigs/grch37_grch38.txt"
+                rename_chr            = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/SV_testdata/grch37_grch38.txt"
             }
         }
     }
@@ -39,7 +39,6 @@ params {
                 high_conf_snv         = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/High-Confidence_Regions_v1.2.bed"
                 truth_indel           = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/high-confidence_sINDEL_in_HC_regions_v1.2.1.vcf.gz"
                 high_conf_indel       = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/seqc/Somatic_Mutation_WG/release/latest/High-Confidence_Regions_v1.2.bed"
-
             }
         }
     }

modules.json

@@ -67,7 +67,7 @@
                     },
                     "happy/sompy": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "5f5f9f7d5508c320124053448ac365fbafc4d3cb",
                         "installed_by": ["modules"]
                     },
                     "manta/convertinversion": {