updated test cases

phac-nml · Nov 6, 2024 · 52af4a9 · 52af4a9
1 parent db5f420
commit 52af4a9
Showing 1 changed file with 9 additions and 9 deletions.
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -209,17 +209,17 @@ nextflow_pipeline {
             // output files
             assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Json/final_report.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Tables/final_report.tsv" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Assembly/FinalAssembly/short/short.final.filtered.assembly.fasta.gz" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Assembly/Quality/QUAST/short/short.transposed_short.quast.quality.tsv" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Assembly/Quality/SeqKitStats/short.seqkit.stats.summary.tsv" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Assembly/PostProcessing/Speciation/MashScreen/short.mash.screen.taxa.screen.screen" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/Trimmed/MashScreen/short.mash.screen.reads.screen.screen" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/Trimmed/FastP/short.fastp.summary.json" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "Reads/Quality/RawReadQuality/short.read.scan.summary.json" }.size() == 1
-            assert iridanext_samples.INX.findAll { it.path == "FinalReports/FlattenedReports/short.flat_sample.json.gz" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Assembly/FinalAssembly/short/short.final.filtered.assembly.fasta.gz" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Assembly/Quality/QUAST/short/short.transposed_short.quast.quality.tsv" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Assembly/Quality/SeqKitStats/short.seqkit.stats.summary.tsv" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Assembly/PostProcessing/Speciation/MashScreen/short.mash.screen.taxa.screen.screen" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Reads/Quality/Trimmed/MashScreen/short.mash.screen.reads.screen.screen" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Reads/Quality/Trimmed/FastP/short.fastp.summary.json" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "Reads/Quality/RawReadQuality/short.read.scan.summary.json" }.size() == 1
+            assert iridanext_samples.short.findAll { it.path == "FinalReports/FlattenedReports/short.flat_sample.json.gz" }.size() == 1
 
             // output metadata
-            assert iridanext_metadata.INX."QC Status" == "PASSED"
+            assert iridanext_metadata.short."QC Status" == "PASSED"
 
         }