nf-core · drpatelh · Jan 29, 2024 · Jan 18, 2024 · Jan 18, 2024 · Jan 18, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -27,19 +27,42 @@ jobs:
  name: Check for changes
  runs-on: ubuntu-latest
  outputs:
- # Expose matched filters as job 'tags' output variable
- tags: ${{ steps.filter.outputs.changes }}
+ changes: ${{ steps.changed_files.outputs.any_modified }}
+ tags: ${{ steps.list.outputs.tags }}
  steps:
+ - name: Install Nextflow
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: "${{ 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.NFT_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/
+
  - uses: actions/checkout@v3
- - name: Combine all tags.yml files
- id: get_username
- run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
- - name: debug
- run: cat .github/tags.yml
- - uses: dorny/paths-filter@v2
- id: filter
  with:
- filters: ".github/tags.yml"
+ fetch-depth: 0
+
+ - uses: tj-actions/changed-files@v42
+ id: changed_files
+ with:
+ dir_names: "true"
+
+ - name: nf-test list tags
+ id: list
+ if: ${{ steps.changed_files.outputs.any_modified }}
+ run: echo tags=$(nf-test list --silent --tags --format json ${{ steps.changed_files.outputs.all_changed_files }}) >> $GITHUB_OUTPUT
 
  define_nxf_versions:
  name: Choose nextflow versions to test against depending on target branch
@@ -56,9 +79,9 @@ jobs:
  fi
 
  test:
- name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+ name: ${{ matrix.tags }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
  needs: [changes, define_nxf_versions]
- if: needs.changes.outputs.tags != '[]'
+ if: needs.changes.outputs.changes
  runs-on: ubuntu-latest
  strategy:
  fail-fast: false

diff --git a/modules/local/multiqc_mappings_config/tests/main.nf.test b/modules/local/multiqc_mappings_config/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
  name "Test process: MULTIQC_MAPPINGS_CONFIG"
  script "../main.nf"
  process "MULTIQC_MAPPINGS_CONFIG"
- tag "modules"
- tag "modules_local"
- tag "multiqc_mappings_config"
+
+ tag "MULTIQC_MAPPINGS_CONFIG"
 
  test("Should run without failures") {
 

diff --git a/modules/local/multiqc_mappings_config/tests/tags.yml b/modules/local/multiqc_mappings_config/tests/tags.yml
diff --git a/modules/local/sra_fastq_ftp/tests/main.nf.test b/modules/local/sra_fastq_ftp/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
  name "Test process: SRA_FASTQ_FTP"
  script "../main.nf"
  process "SRA_FASTQ_FTP"
- tag "modules"
- tag "modules_local"
- tag "sra_fastq_ftp"
+
+ tag "SRA_FASTQ_FTP"
 
  test("Should run without failures") {
 

diff --git a/modules/local/sra_fastq_ftp/tests/tags.yml b/modules/local/sra_fastq_ftp/tests/tags.yml
diff --git a/modules/local/sra_ids_to_runinfo/tests/main.nf.test b/modules/local/sra_ids_to_runinfo/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
  name "Test process: SRA_IDS_TO_RUNINFO"
  script "../main.nf"
  process "SRA_IDS_TO_RUNINFO"
- tag "modules"
- tag "modules_local"
- tag "sra_ids_to_runinfo"
+
+ tag "SRA_IDS_TO_RUNINFO"
 
  test("Should run without failures") {
 

diff --git a/modules/local/sra_ids_to_runinfo/tests/tags.yml b/modules/local/sra_ids_to_runinfo/tests/tags.yml
diff --git a/modules/local/sra_runinfo_to_ftp/tests/main.nf.test b/modules/local/sra_runinfo_to_ftp/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
  name "Test process: SRA_RUNINFO_TO_FTP"
  script "../main.nf"
  process "SRA_RUNINFO_TO_FTP"
- tag "modules"
- tag "modules_local"
- tag "sra_runinfo_to_ftp"
+
+ tag "SRA_RUNINFO_TO_FTP"
 
  test("Should run without failures") {
 

diff --git a/modules/local/sra_runinfo_to_ftp/tests/tags.yml b/modules/local/sra_runinfo_to_ftp/tests/tags.yml
diff --git a/modules/local/sra_to_samplesheet/tests/main.nf.test b/modules/local/sra_to_samplesheet/tests/main.nf.test
@@ -3,9 +3,8 @@ nextflow_process {
  name "Test process: SRA_TO_SAMPLESHEET"
  script "../main.nf"
  process "SRA_TO_SAMPLESHEET"
- tag "modules"
- tag "modules_local"
- tag "sra_to_samplesheet"
+
+ tag "SRA_TO_SAMPLESHEET"
 
  test("Should run without failures") {
 

diff --git a/modules/local/sra_to_samplesheet/tests/tags.yml b/modules/local/sra_to_samplesheet/tests/tags.yml
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test b/modules/nf-core/custom/sratoolsncbisettings/tests/main.nf.test
diff --git a/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml b/modules/nf-core/custom/sratoolsncbisettings/tests/tags.yml
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
diff --git a/modules/nf-core/sratools/fasterqdump/tests/tags.yml b/modules/nf-core/sratools/fasterqdump/tests/tags.yml
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
diff --git a/modules/nf-core/sratools/prefetch/tests/tags.yml b/modules/nf-core/sratools/prefetch/tests/tags.yml
diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test
diff --git a/modules/nf-core/untar/tests/tags.yml b/modules/nf-core/untar/tests/tags.yml
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/main.nf.test
diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.functions.nf.test
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test
diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -2,8 +2,10 @@ nextflow_pipeline {
 
  name "Test pipeline"
  script "../main.nf"
- tag "pipeline"
- tag "pipeline_fetchngs"
+
+ tag "FETCHNGS"
+
+ tag "SRA"
 
  test("Run with profile test") {
 

diff --git a/tests/tags.yml b/tests/tags.yml
diff --git a/workflows/sra/tests/main.nf.test b/workflows/sra/tests/main.nf.test
@@ -3,10 +3,18 @@ nextflow_workflow {
  name "Test workflow: sra/main.nf"
  script "../main.nf"
  workflow "SRA"
- tag "workflows"
- tag "workflows_sra"
- tag "multiqc_mappings_config"
- tag "sra_default_parameters"
+
+
+ // Subworkflows
- // Subworkflows
+ // Workflow
- // Subworkflows
+ // Workflow
+ tag "SRA"
+
+ // Modules
- // Modules
+ // Dependencies
- // Modules
+ // Dependencies
+ tag "MULTIQC_MAPPINGS_CONFIG"
+ tag "SRA_FASTQ_FTP"
+ tag "SRA_IDS_TO_RUNINFO"
+ tag "SRA_RUNINFO_TO_FTP"
+ tag "SRA_TO_SAMPLESHEET"
+
 
  test("Parameters: default") {
 

diff --git a/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test b/workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
  name "Test workflow: sra/main.nf"
  script "../main.nf"
  workflow "SRA"
- tag "workflows"
- tag "workflows_sra"
- tag "multiqc_mappings_config"
- tag "sra_custom_ena_metadata_fields"
+
+ // Subworkflows
+ tag "SRA"
+
+ // Modules
+ tag "MULTIQC_MAPPINGS_CONFIG"
+ tag "SRA_FASTQ_FTP"
+ tag "SRA_IDS_TO_RUNINFO"
+ tag "SRA_RUNINFO_TO_FTP"
+ tag "SRA_TO_SAMPLESHEET"
 
  test("Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ...") {
 

diff --git a/workflows/sra/tests/sra_force_sratools_download.nf.test b/workflows/sra/tests/sra_force_sratools_download.nf.test
@@ -3,10 +3,16 @@ nextflow_workflow {
  name "Test workflow: sra/main.nf"
  script "../main.nf"
  workflow "SRA"
- tag "workflows"
- tag "workflows_sra"
- tag "multiqc_mappings_config"
- tag "sra_force_sratools_download"
+
+ // Subworkflows
+ tag "SRA"
+
+ // Modules
+ tag "MULTIQC_MAPPINGS_CONFIG"
+ tag "SRA_FASTQ_FTP"
+ tag "SRA_IDS_TO_RUNINFO"
+ tag "SRA_RUNINFO_TO_FTP"
+ tag "SRA_TO_SAMPLESHEET"
 
  test("Parameters: --force_sratools_download") {