add very simple tests

nf-core · May 17, 2024 · f36cbdf · f36cbdf
1 parent d1c5d0e
commit f36cbdf
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Showing 2 changed files with 18 additions and 52 deletions.
diff --git a/tests/pipeline/bismark/samplesheet.nf.test b/tests/pipeline/bismark/samplesheet.nf.test
@@ -5,66 +5,20 @@ nextflow_pipeline {
 
     tag "pipeline"
 
-
-    test("Should ____") {
+    test("Should handle replicates and works") {
         when {
             params {
-                input = "$baseDir/tests/pipeline/bismark/assets/samplesheet.csv"
-                outdir = "$outputDir"
+                aligner        = "bismark"
+                save_reference = true
+                input          = "$baseDir/tests/pipeline/bismark/assets/samplesheet.csv"
+                outdir         = "$outputDir"
             }
         }
 
         then {
             assertAll(
-                { assert workflow.success },
-                // TODO Output names should be as expected
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("single_end_software_versions") },
-                { assert snapshot(path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.flagstat"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/Ecoli.stats"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.flagstat"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub1.stats"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.flagstat"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub2.stats"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat"),
-                            path("$outputDir/bwameth/alignments/samtools_stats/SRR389222_sub3.stats"),
-                            path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam"),
-                            path("$outputDir/bwameth/deduplicated/Ecoli.markdup.sorted.bam.bai"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam"),
-                            path("$outputDir/bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai"),
-                            path("$outputDir/bwameth/reference_genome/").list(),
-                            path("$outputDir/methyldackel/Ecoli.markdup.sorted_CpG.bedGraph"),
-                            path("$outputDir/methyldackel/SRR389222_sub1.markdup.sorted_CpG.bedGraph"),
-                            path("$outputDir/methyldackel/SRR389222_sub2.markdup.sorted_CpG.bedGraph"),
-                            path("$outputDir/methyldackel/SRR389222_sub3.markdup.sorted_CpG.bedGraph"),
-                            path("$outputDir/methyldackel/mbias/Ecoli.mbias.txt"),
-                            path("$outputDir/methyldackel/mbias/SRR389222_sub1.mbias.txt"),
-                            path("$outputDir/methyldackel/mbias/SRR389222_sub2.mbias.txt"),
-                            path("$outputDir/methyldackel/mbias/SRR389222_sub3.mbias.txt"),
-                            path("$outputDir/qualimap/Ecoli/genome_results.txt"),
-                            path("$outputDir/qualimap/SRR389222_sub1/genome_results.txt"),
-                            path("$outputDir/qualimap/SRR389222_sub2/genome_results.txt"),
-                            path("$outputDir/qualimap/SRR389222_sub3/genome_results.txt")).match("single_end") },
-                { assert new File("$outputDir/fastqc/Ecoli_1_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/Ecoli_2_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/SRR389222_sub1_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/SRR389222_sub2_fastqc.html").exists() },
-                { assert new File("$outputDir/fastqc/SRR389222_sub3_fastqc.html").exists() },
-                { assert new File("$outputDir/multiqc/bwameth/multiqc_report.html").exists() },
-                { assert new File("$outputDir/trimgalore/logs/Ecoli_1.fastq.gz_trimming_report.txt").exists() },
-                { assert new File("$outputDir/trimgalore/logs/Ecoli_2.fastq.gz_trimming_report.txt").exists() },
-                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub1.fastq.gz_trimming_report.txt").exists() },
-                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub2.fastq.gz_trimming_report.txt").exists() },
-                { assert new File("$outputDir/trimgalore/logs/SRR389222_sub3.fastq.gz_trimming_report.txt").exists() },
-                { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/Ecoli.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
-                { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub1.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
-                { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub2.markdup.sorted.MarkDuplicates.metrics.txt").exists() },
-                { assert new File("$outputDir/bwameth/deduplicated/picard_metrics/SRR389222_sub3.markdup.sorted.MarkDuplicates.metrics.txt").exists() }
+                { assert workflow.success }
             )
         }
     }
-
 }
diff --git a/tests/pipeline/bismark/samplesheet.nf.test.snap b/tests/pipeline/bismark/samplesheet.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "single_end_software_versions": {
+        "content": [
+            "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, Workflow={nf-core/methylseq=v2.7.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.0"
+        },
+        "timestamp": "2024-05-17T14:37:44.368983"
+    }
+}