Merge pull request #51 from kedhammar/ci-nf-test

kedhammar · web-flow · commit a2d589f3a2c6 · 2024-10-29T16:49:12.000+01:00
Add nf-test to CI
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -0,0 +1,32 @@
+name: nf-test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        shard: [1, 2, 3, 4]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: "11"
+          distribution: "adopt"
+
+      - name: Setup Nextflow latest-edge
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- https://get.nf-test.com | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }} .
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
 - [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
 - [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
 
 ### `Fixed`
 
diff --git a/modules.json b/modules.json
@@ -21,7 +21,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -31,7 +31,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }
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_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test
diff --git a/tests/MiSeq.main.nf.test b/tests/MiSeq.main.nf.test
@@ -21,7 +21,6 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 }
             )
diff --git a/tests/MiSeq.main.nf.test.snap b/tests/MiSeq.main.nf.test.snap
@@ -3,13 +3,12 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7b1b7fd457b60404768045b148d4c0a8",
-            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,5b28a83b14cb2fe88d084d08900ebdbf"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
         "timestamp": "2024-10-28T13:18:10.3675973"
     }
-}
+}
diff --git a/tests/NovaSeq6000.main.nf.test b/tests/NovaSeq6000.main.nf.test
@@ -21,27 +21,22 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/lane1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group1/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/group2/multiqc_data/multiqc_software_versions.txt"),
 
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/group_reports/test/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/NovaSeq6000.main.nf.test.snap b/tests/NovaSeq6000.main.nf.test.snap
@@ -4,28 +4,23 @@
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,3730f9046b20ac5c17a86db0a33f8d5d",
             "multiqc_general_stats.txt:md5,25abe0f6a35eb4a3b056fc3cf5c13732",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,8284e25ccc21041cf3b5a32eb6a51e78",
             "multiqc_general_stats.txt:md5,90ee35137492b80aab36ef67f72d8921",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,f38ffdc112c73af3a41ed15848a3761f",
             "multiqc_general_stats.txt:md5,d62a2fc39e674d98783d408791803148",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,7ff71ceb8ecdf086331047f8860c3347",
             "multiqc_general_stats.txt:md5,2f09b8f199ac40cf67ba50843cebd29c",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3",
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,519ff344a896ac369bba4d5c5b8be7b5",
-            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,6a1c16f068d7ba3a9225a17eb570ed9a"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
         "timestamp": "2024-10-28T13:19:13.226135825"
     }
-}
+}
diff --git a/tests/PromethION.main.nf.test b/tests/PromethION.main.nf.test
@@ -21,7 +21,6 @@ nextflow_pipeline {
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),
                     path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),
                     ).match()
                 },
             )
diff --git a/tests/PromethION.main.nf.test.snap b/tests/PromethION.main.nf.test.snap
@@ -3,13 +3,12 @@
         "content": [
             "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
             "multiqc_fastqc.txt:md5,1a4b472e13cadc770832b0e20d1de7b0",
-            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32",
-            "multiqc_software_versions.txt:md5,a3698a2d32e8695c38d50e3d17de5fe3"
+            "multiqc_general_stats.txt:md5,409cefc7f17f95d176ced6032bf8fb32"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.10.0"
         },
         "timestamp": "2024-10-28T13:19:57.261730412"
     }
-}
+}
diff --git a/tests/nextflow.config b/tests/nextflow.config
@@ -8,14 +8,8 @@ params {
     config_profile_name        = 'nf-test profile'
     config_profile_description = 'Configuration profile to use for nf-test.'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '3.GB'
-    max_time   = '2.h'
-
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    modules_testdata_base_path   = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
     validationSchemaIgnoreParams = 'genomes,igenomes_base,pipelines_testdata_base_path'
-
-
 }
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
@@ -87,10 +87,10 @@ workflow SEQINSPECTOR {
             .mix(ch_multiqc_extra_files)
             .collect(),
         ch_multiqc_config.toList(),
-        Channel.empty().toList(),
+        [],
         ch_multiqc_logo.toList(),
-        Channel.empty().toList(),
-        Channel.empty().toList()
+        [],
+        []
     )
 
     ch_tags = ch_multiqc_files
@@ -138,9 +138,9 @@ workflow SEQINSPECTOR {
     )
 
     emit:
-    global_report = MULTIQC_GLOBAL.out.report.toList()      // channel: /path/to/multiqc_report.html
+    global_report   = MULTIQC_GLOBAL.out.report.toList()    // channel: [ /path/to/multiqc_report.html ]
     grouped_reports = MULTIQC_PER_TAG.out.report.toList()   // channel: [ /path/to/multiqc_report.html ]
-    versions       = ch_versions                            // channel: [ path(versions.yml) ]
+    versions        = ch_versions                           // channel: [ path(versions.yml) ]
 }
 
 /*

Original file line number	Diff line number	Diff line change
`@@ -21,7 +21,6 @@ nextflow_pipeline {`
`21`	`21`	`path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),`
`22`	`22`	`path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt"),`
`23`	`23`	`path("$outputDir/multiqc/global_report/multiqc_data/multiqc_general_stats.txt"),`
`24`		`- path("$outputDir/multiqc/global_report/multiqc_data/multiqc_software_versions.txt"),`
`25`	`24`	`).match()`
`26`	`25`	`}`
`27`	`26`	`)`