Update tests and relevant GH Actions workflows / actions

.github/actions/nf-test/action.yml

@@ -70,8 +70,8 @@ runs:
           --tap=test.tap \
           --shard ${{ inputs.shard }}/${{ inputs.total_shards }}
 
-          # Save the absolute path of the test.tap file to the output
-          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+        # Save the absolute path of the test.tap file to the output
+        echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
 
     - name: Generate test summary
       if: always()

.github/workflows/awsfulltest.yml

@@ -24,9 +24,6 @@ jobs:
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/nf-test-entry.yml

@@ -0,0 +1,76 @@
+name: Run nf-test
+on:
+  pull_request:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  release:
+    types: [published]
+  workflow_dispatch:
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # NOTE(SW): only run large tests on up-sized instances to avoid wasting compute (in this case the just test profile)
+  # NOTE(SW): the test profile requires more than 32 GB memory and with the available RunsOn instances, the 32cpu-linux-x64 runner is the best fit despite being excessively overprovisioned re vCPUs
+  # https://runs-on.com/runners/linux/
+  # Instance type     vCPUs   Memory (GiB)  RunsOn name
+  # m7a.medium            1              4  1cpu-linux-x64
+  # m7i.large             2              8  2cpu-linux-x64
+  # m7i.xlarge            4             16  4cpu-linux-x64
+  # c7i.2xlarge           8             16  8cpu-linux-x64
+  # c7i.4xlarge          16             32  16cpu-linux-x64
+  # m7i-flex.8xlarge     32            128  32cpu-linux-x64
+  # c7i.12xlarge         48             96  48cpu-linux-x64
+  # c7a.16xlarge         64            128  64cpu-linux-x64
+  nf-test:
+    uses: ./.github/workflows/nf-test-reusable.yml
+    strategy:
+      matrix:
+        include:
+          - name: small
+            tags: cicd
+            runson_instance_type: 4cpu-linux-x64
+            runson_volume_size: 60gb
+          - name: large
+            tags: cicd.large
+            runson_instance_type: 32cpu-linux-x64
+            runson_volume_size: 200gb
+    with:
+      name: ${{ matrix.name }}
+      tags: ${{ matrix.tags }}
+      runson_instance_type: ${{ matrix.runson_instance_type }}
+      runson_volume_size: ${{ matrix.runson_volume_size }}
+
+  confirm-pass:
+    needs: [nf-test]
+    if: always()
+    runs-on: # use self-hosted runners
+      - runs-on=${{ github.run_id }}-confirm-pass
+      - runner=1cpu-linux-x64
+    steps:
+      - name: One or more tests failed (excluding latest-everything)
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"

.github/workflows/nf-test.yml → .github/workflows/nf-test-reusable.yml

@@ -1,24 +1,26 @@
-name: Run nf-test
+name: Run nf-test on selected test set
 on:
-  pull_request:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
-  release:
-    types: [published]
-  workflow_dispatch:
-
-# Cancel if a newer run is started
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
+  workflow_call:
+    inputs:
+      name:
+        description: "Name of test set"
+        type: string
+        required: true
+      tags:
+        description: "Tags to pass as argument for nf-test --tag parameter"
+        type: string
+        required: true
+      runson_instance_type:
+        description: "RunsOn runner instance type"
+        type: string
+        required: true
+      runson_volume_size:
+        description: "RunsOn runner instance volume"
+        type: string
+        required: true
 
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  NFT_TAGS: "cicd"
   NFT_VER: "0.9.3"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
@@ -27,10 +29,10 @@ env:
 
 jobs:
   nf-test-changes:
-    name: nf-test-changes
+    name: nf-test-changes (${{ inputs.name }})
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test-changes
-      - runner=4cpu-linux-x64
+      - runner=1cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
       total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -52,21 +54,21 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
         with:
           max_shards: 7
-          tags: ${{ env.NFT_TAGS }}
+          tags: ${{ inputs.tags }}
 
       - name: debug
         run: |
           echo ${{ steps.set-shards.outputs.shard }}
           echo ${{ steps.set-shards.outputs.total_shards }}
 
   nf-test:
-    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    name: " ${{ inputs.name }} tests | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
-      - runner=4cpu-linux-x64
-      - disk=large
+      - runner=${{ inputs.runson_instance_type }}
+      - volume=${{ inputs.runson_volume_size }}
     strategy:
       fail-fast: false
       matrix:
@@ -103,7 +105,7 @@ jobs:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
-          tags: ${{ env.NFT_TAGS }}
+          tags: ${{ inputs.tags }}
 
       - name: Report test status
         if: ${{ always() }}
@@ -119,30 +121,3 @@ jobs:
               exit 1
             fi
           fi
-
-  confirm-pass:
-    needs: [nf-test]
-    if: always()
-    runs-on: # use self-hosted runners
-      - runs-on=${{ github.run_id }}-confirm-pass
-      - runner=2cpu-linux-x64
-    steps:
-      - name: One or more tests failed (excluding latest-everything)
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: One or more tests cancelled
-        if: ${{ contains(needs.*.result, 'cancelled') }}
-        run: exit 1
-
-      - name: All tests ok
-        if: ${{ contains(needs.*.result, 'success') }}
-        run: exit 0
-
-      - name: debug-print
-        if: always()
-        run: |
-          echo "::group::DEBUG: `needs` Contents"
-          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
-          echo "::endgroup::"

.nf-core.yml

@@ -15,6 +15,7 @@ template:
 lint:
   actions_ci: false
   files_exist:
+    - .github/workflows/nf-test.yml
     - lib/Utils.groovy
     - lib/WorkflowMain.groovy
     - lib/WorkflowOncoanalyser.groovy

conf/test_full.config

@@ -10,18 +10,12 @@
 ----------------------------------------------------------------------------------------
 */
 
-process {
-    withName: 'PURPLE' {
-        ext.args = '-min_purity 1 -max_purity 1 -min_ploidy 2 -max_ploidy 2'
-    }
-}
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = params.pipelines_testdata_base_path + '/samplesheet/fastq_eval.subject_a.wgts.tndna_trna.minimal.csv'
+    input = params.pipelines_testdata_base_path + '/samplesheet/full_size.hcc1395.wgts.tndna_trna.fastq.csv'
 
     // Analysis config
     mode              = 'wgts'

tests/default.nf.test.snap

@@ -21,29 +21,29 @@
                 "subject_a/amber",
                 "subject_a/amber/placeholder",
                 "subject_a/bamtools",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.coverage.tsv",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.flag_counts.tsv",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.frag_length.tsv",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.partition_stats.tsv",
-                "subject_a/bamtools/subject_a_subject_a.normal_bamtools/subject_a.normal.bam_metric.summary.tsv",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.coverage.tsv",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.flag_counts.tsv",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.frag_length.tsv",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.partition_stats.tsv",
-                "subject_a/bamtools/subject_a_subject_a.tumor_bamtools/subject_a.tumor.bam_metric.summary.tsv",
+                "subject_a/bamtools/subject_a.normal",
+                "subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.coverage.tsv",
+                "subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.flag_counts.tsv",
+                "subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.frag_length.tsv",
+                "subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.partition_stats.tsv",
+                "subject_a/bamtools/subject_a.normal/subject_a.normal.bam_metric.summary.tsv",
+                "subject_a/bamtools/subject_a.tumor",
+                "subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.coverage.tsv",
+                "subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.flag_counts.tsv",
+                "subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.frag_length.tsv",
+                "subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.partition_stats.tsv",
+                "subject_a/bamtools/subject_a.tumor/subject_a.tumor.bam_metric.summary.tsv",
                 "subject_a/chord",
                 "subject_a/chord/subject_a.tumor.chord.mutation_contexts.tsv",
                 "subject_a/chord/subject_a.tumor.chord.prediction.tsv",
                 "subject_a/cider",
+                "subject_a/cider/subject_a.tumor.cider.alignment_match.tsv.gz",
                 "subject_a/cider/subject_a.tumor.cider.bam",
-                "subject_a/cider/subject_a.tumor.cider.blastn_match.tsv.gz",
                 "subject_a/cider/subject_a.tumor.cider.layout.gz",
                 "subject_a/cider/subject_a.tumor.cider.locus_stats.tsv",
                 "subject_a/cider/subject_a.tumor.cider.vdj.tsv.gz",
+                "subject_a/cider/subject_a.tumor_rna.cider.alignment_match.tsv.gz",
                 "subject_a/cider/subject_a.tumor_rna.cider.bam",
-                "subject_a/cider/subject_a.tumor_rna.cider.blastn_match.tsv.gz",
                 "subject_a/cider/subject_a.tumor_rna.cider.layout.gz",
                 "subject_a/cider/subject_a.tumor_rna.cider.locus_stats.tsv",
                 "subject_a/cider/subject_a.tumor_rna.cider.vdj.tsv.gz",
@@ -277,6 +277,23 @@
                 "subject_a/purple/subject_a.tumor.purple.somatic.vcf.gz",
                 "subject_a/purple/subject_a.tumor.purple.sv.germline.vcf.gz",
                 "subject_a/purple/subject_a.tumor.purple.sv.vcf.gz",
+                "subject_a/sage",
+                "subject_a/sage/germline",
+                "subject_a/sage/germline/subject_a.normal.gene.coverage.tsv",
+                "subject_a/sage/germline/subject_a.normal.sage.bqr.png",
+                "subject_a/sage/germline/subject_a.normal.sage.bqr.tsv",
+                "subject_a/sage/germline/subject_a.tumor.sage.bqr.png",
+                "subject_a/sage/germline/subject_a.tumor.sage.bqr.tsv",
+                "subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz",
+                "subject_a/sage/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
+                "subject_a/sage/somatic",
+                "subject_a/sage/somatic/subject_a.normal.sage.bqr.png",
+                "subject_a/sage/somatic/subject_a.normal.sage.bqr.tsv",
+                "subject_a/sage/somatic/subject_a.tumor.gene.coverage.tsv",
+                "subject_a/sage/somatic/subject_a.tumor.sage.bqr.png",
+                "subject_a/sage/somatic/subject_a.tumor.sage.bqr.tsv",
+                "subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz",
+                "subject_a/sage/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
                 "subject_a/sage_append",
                 "subject_a/sage_append/germline",
                 "subject_a/sage_append/germline/subject_a.normal.frag_lengths.tsv.gz",
@@ -288,23 +305,6 @@
                 "subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz",
                 "subject_a/sage_append/somatic/subject_a.tumor.sage.append.vcf.gz.tbi",
                 "subject_a/sage_append/somatic/subject_a.tumor_query.sage.bqr.tsv",
-                "subject_a/sage_calling",
-                "subject_a/sage_calling/germline",
-                "subject_a/sage_calling/germline/subject_a.normal.gene.coverage.tsv",
-                "subject_a/sage_calling/germline/subject_a.normal.sage.bqr.png",
-                "subject_a/sage_calling/germline/subject_a.normal.sage.bqr.tsv",
-                "subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.png",
-                "subject_a/sage_calling/germline/subject_a.tumor.sage.bqr.tsv",
-                "subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz",
-                "subject_a/sage_calling/germline/subject_a.tumor.sage.germline.vcf.gz.tbi",
-                "subject_a/sage_calling/somatic",
-                "subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.png",
-                "subject_a/sage_calling/somatic/subject_a.normal.sage.bqr.tsv",
-                "subject_a/sage_calling/somatic/subject_a.tumor.gene.coverage.tsv",
-                "subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.png",
-                "subject_a/sage_calling/somatic/subject_a.tumor.sage.bqr.tsv",
-                "subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz",
-                "subject_a/sage_calling/somatic/subject_a.tumor.sage.somatic.vcf.gz.tbi",
                 "subject_a/sigs",
                 "subject_a/sigs/placeholder",
                 "subject_a/teal",
@@ -323,9 +323,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-08-12T16:05:52.737409"
+        "timestamp": "2025-12-03T04:25:08.751931146"
     }
 }

tests/profile_test.nf.test

@@ -3,6 +3,7 @@ nextflow_pipeline {
     name "Test pipeline"
     script "../main.nf"
     tag "pipeline"
+    tag "cicd.large"
 
     profile "test"