nf-test POC

.gitattributes

@@ -1,4 +1,5 @@
 *.config linguist-language=nextflow
 *.nf.test linguist-language=nextflow
+tests/**/*nf.test.snap linguist-generated
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/tags.yml

@@ -0,0 +1,71 @@
+# local modules
+multiqc_mappings_config:
+  - modules/local/multiqc_mappings_config/**
+sra_fastq_ftp:
+  - modules/local/sra_fastq_ftp/**
+sra_ids_to_runinfo:
+  - modules/local/sra_ids_to_runinfo/**
+sra_merge_samplesheet:
+  - modules/local/sra_merge_samplesheet/**
+sra_runinfo_to_ftp:
+  - modules/local/sra_runinfo_to_ftp/**
+sra_to_samplesheet:
+  - modules/local/sra_to_samplesheet/**
+
+# workflow: sra
+sra_custom_ena_metadata_fields:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_default_parameters:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_force_sratools_download:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_nf_core_pipeline_atacseq:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_nf_core_pipeline_rnaseq:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_nf_core_pipeline_taxprofiler:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_nf_core_pipeline_viralrecon:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**
+sra_skip_fastq_download:
+  - modules/local/sra_ids_to_runinfo/**
+  - modules/local/sra_runinfo_to_ftp/**
+  - modules/local/sra_fastq_ftp/**
+  - modules/local/sra_to_samplesheet/**
+  - modules/local/sra_merge_samplesheet/**
+  - workflows/sra/**

.github/workflows/ci.yml

@@ -1,28 +1,67 @@
-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:
   pull_request:
   release:
     types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
+      - refactor
+      - nf-test
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.0-rc2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
+  changes:
+    name: Check for changes
+    runs-on: ubuntu-latest
+    outputs:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: ".github/tags.yml"
+
+  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 $GITHUB_OUTPUT
+          fi
+
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}"
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    needs: [changes, define_nxf_versions]
+    if: needs.changes.outputs.tags != '[]'
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile:
+          - "docker"
+
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -32,29 +71,23 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
+      - name: Install nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
+          sudo mv nf-test /usr/local/bin/
 
-  parameters:
-    name: Test workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/fetchngs') }}
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        parameters:
-          - "--nf_core_pipeline rnaseq"
-          - "--ena_metadata_fields run_accession,experiment_accession,library_layout,fastq_ftp,fastq_md5 --sample_mapping_fields run_accession,library_layout"
-          - "--skip_fastq_download"
-          - "--force_sratools_download"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v2
-
-      - name: Install Nextflow
+      - name: Run nf-test
         run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
-      - name: Run pipeline with various parameters
+          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
+          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

.gitignore

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

.nf-core.yml

@@ -10,3 +10,4 @@ lint:
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy
+    - .gitattributes

conf/test_data.config

@@ -0,0 +1,36 @@
+params {
+    // Base directory for test data
+    test_data_base = "https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs"
+
+    merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]
+
+    def merge_samplesheet_url  = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
+    def merge_mappings_url     = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
+    def merge_samplesheet_urls = []
+    def merge_mappings_urls    = []
+
+    merge_samplesheet_ids.each { id ->
+        merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
+        merge_mappings_urls    += "${merge_mappings_url}/${id}.mappings.csv"
+    }
+
+    fastq_ftp_ids      = ["SRR13191702"]
+    def fastq_ftp_url  = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
+    def fastq_ftp_urls = []
+
+    fastq_ftp_ids.each { id ->
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
+        fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
+    }
+
+    test_data {
+        'modules_local' {
+                multiqc_mappings_config             = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
+                sra_merge_samplesheet_samplesheets  = merge_samplesheet_urls
+                sra_merge_samplesheet_mappings      = merge_mappings_urls
+                sra_to_samplesheet                  = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
+                sra_fastq_ftp                       = fastq_ftp_urls
+                sra_runinfo_to_ftp                  = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
+        }
+    }
+}

modules/local/multiqc_mappings_config/tests/main.nf.test

@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test process: MULTIQC_MAPPINGS_CONFIG"
+    script "modules/local/multiqc_mappings_config/main.nf"
+    process "MULTIQC_MAPPINGS_CONFIG"
+    tag "modules"
+    tag "modules_local"
+    tag "multiqc_mappings_config"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = file(params.test_data['modules_local']['multiqc_mappings_config'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/local/multiqc_mappings_config/tests/main.nf.test.snap

@@ -0,0 +1,27 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                ],
+                "yml": [
+                    [
+                        "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
+                        "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2023-09-22T10:58:18.132284"
+    }
+}

modules/local/sra_fastq_ftp/tests/main.nf.test

@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test process: SRA_FASTQ_FTP"
+    script "modules/local/sra_fastq_ftp/main.nf"
+    process "SRA_FASTQ_FTP"
+    tag "modules"
+    tag "modules_local"
+    tag "sra_fastq_ftp"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    params.test_data['modules_local']['sra_fastq_ftp']
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}