update docs

.github/CONTRIBUTING.md

@@ -82,6 +82,12 @@ If you wish to contribute a new step, please use the following coding standards:
 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
+### Things to consider regarding displaying results for a new tool
+
+- If a MultiQC module exist for the tool, use the standard settings for it to start with.
+- If no Multiqc module exists, the results of the tool should be made available in the results directory.
+- If a tool doesn’t produce output files, the stdout should be channeled into a output file that can be accessible from the outdir of the pipeline.
+
 ### Default values
 
 Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

.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 }} .

.nf-core.yml

@@ -1,5 +1,7 @@
 bump_version: null
-lint: null
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline

CHANGELOG.md

@@ -12,7 +12,11 @@ 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.
-- [#40](https://github.com/nf-core/seqinspector/pull/59) Seqkit Stats TSV output.
+  <<<<<<< HEAD
+- # [#40](https://github.com/nf-core/seqinspector/pull/59) Seqkit Stats TSV output.
+- [#51](https://github.com/nf-core/seqinspector/pull/51) Add nf-test to CI.
+- [#63](https://github.com/nf-core/seqinspector/pull/63) Contribution guidelines added about displaying results for new tools
+  > > > > > > > 1ca5e188c2fc4f501b3bb123e97ebfc743ae5b06
 
 ### `Fixed`
 

docs/output.md

@@ -70,7 +70,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 
 </details>
 
-[SeqkitStats](https://bioinf.shenwei.me/seqkit/usage/#stats) it gives general quality metrics about your sequenced reads including average read lengths, GC(%) and n50's. For further reading and documentation see the [Seqkit help pages]([Seqkit help](https://bioinf.shenwei.me/seqkit/)).
+[SeqkitStats](https://bioinf.shenwei.me/seqkit/usage/#stats) it gives simple statistics such as number of sequences, min/max_len, N50, Q20%, Q30% and GC%. For further reading and documentation see the [Seqkit help pages]([Seqkit help](https://bioinf.shenwei.me/seqkit/)).
 
 ### Pipeline information
 

modules.json

@@ -26,7 +26,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "56372688d8979092cafbe0c5c3895b491166ca1c",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -36,7 +36,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

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()
                 }
             )

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"
     }
-}
+}

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()
                 },
             )

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"
     }
-}
+}

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()
                 },
             )

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"
     }
-}
+}

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'
-
-
 }

workflows/seqinspector.nf

@@ -89,10 +89,10 @@ 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
@@ -148,9 +148,9 @@ workflow SEQINSPECTOR {
     ch_versions = ch_versions.mix(SEQKIT_STATS.out.versions.first())
 
     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) ]
 }
 
 /*