Merge pull request #75 from Aratz/nft-utils

Set up nft-utils in tests

CHANGELOG.md

@@ -9,6 +9,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 
 ### `Added`
 
+- [#75](https://github.com/nf-core/seqinspector/pull/75) Set up nft-utils
 - [#68](https://github.com/nf-core/seqinspector/pull/68) Add tool selector
 - [#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.

nf-test.config

@@ -5,4 +5,7 @@ config {
     configFile "tests/nextflow.config"
     profile "test,docker"
 
+    plugins {
+        load "[email protected]"
+    }
 }

tests/.nftignore

@@ -0,0 +1,12 @@
+.DS_Store
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc.log
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_data.json
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_general_stats.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_software_versions.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/multiqc_sources.txt
+multiqc/{global_report,group_reports/*}/multiqc_data/fastqc_top_overrepresented_sequences_table.txt
+multiqc/{global_report,group_reports/*}/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png}
+multiqc/{global_report,group_reports/*}/multiqc_report.html
+pipeline_info/*.{html,json,txt,yml}
+fastqscreen/*_screen.html
+fastqc/*_fastqc.{html,zip}

tests/MiSeq.main.nf.test

@@ -15,15 +15,28 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$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("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastq_screen.txt"),
-                    ).match()
-                }
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }
@@ -38,15 +51,64 @@ nextflow_pipeline {
         }
 
         then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+
+    test("Miseq data test (skip all tools)") {
+        when {
+            config "./MiSeq.main.nf.test.config"
+            params {
+                outdir = "$outputDir"
+                skip_tools = "fastqc,fastqscreen,seqfu_stats,seqtk_sample"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(
+                params.outdir,
+                relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']
+            )
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(
+                params.outdir,
+                ignoreFile: 'tests/.nftignore'
+            )
             assertAll(
-                { assert workflow.success },
+                { assert workflow.success},
                 { assert snapshot(
-                    path("$outputDir/multiqc/global_report/multiqc_data/multiqc_citations.txt"),
-                    ).match()
-                },
-                {
-                    assert !path("$outputDir/multiqc/global_report/multiqc_data/multiqc_fastqc.txt").exists()
-                }
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_seqinspector_software_mqc_versions.yml"),
+                    // All stable path names, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
             )
         }
     }