update .nf.test files

nf-core · Jul 27, 2023 · e30f162 · e30f162
1 parent a1002f7
commit e30f162
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Showing 12 changed files with 23 additions and 12 deletions.
diff --git a/conf/test_doubleprimers.config b/conf/test_doubleprimers.config
@@ -23,7 +23,7 @@ params {
     FW_primer = "NNNNCCTAHGGGRBGCAGCAG"
     RV_primer = "GACTACHVGGGTATCTAATCC"
     double_primer = true
-    dada_ref_taxonomy = false
+    skip_dada_taxonomy = true
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet_double_primer.tsv"
     trunc_qmin = 30
     skip_fastqc = true

diff --git a/tests/pipeline/doubleprimers.nf.test b/tests/pipeline/doubleprimers.nf.test
@@ -33,7 +33,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/qiime2/input/table.qza").exists() },
                 { assert snapshot(path("$outputDir/input/Samplesheet_double_primer.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/fasta.nf.test b/tests/pipeline/fasta.nf.test
@@ -25,7 +25,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/dada2/ref_taxonomy.rdp_18.txt")).match("dada2") },
                 { assert new File("$outputDir/dada2/ASV_tax_species.rdp_18.tsv").exists() },
                 { assert new File("$outputDir/dada2/ASV_tax.rdp_18.tsv").exists() },
-                { assert snapshot(path("$outputDir/input/ASV_seqs.fasta")).match("input") }
+                { assert snapshot(path("$outputDir/input/ASV_seqs.fasta")).match("input") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/iontorrent.nf.test b/tests/pipeline/iontorrent.nf.test
@@ -38,7 +38,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/input/Samplesheet_it_SE_ITS.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/multi.nf.test b/tests/pipeline/multi.nf.test
@@ -63,7 +63,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/qiime2/representative_sequences/filtered-sequences.qza").exists() },
                 { assert new File("$outputDir/qiime2/representative_sequences/rep-seq.fasta").exists() },
                 { assert snapshot(path("$outputDir/qiime2/representative_sequences/descriptive_stats.tsv"),
-                                path("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv")).match("qiime2") }
+                                path("$outputDir/qiime2/representative_sequences/seven_number_summary.tsv")).match("qiime2") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/novaseq.nf.test b/tests/pipeline/novaseq.nf.test
@@ -28,7 +28,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/fastqc/S2_2_fastqc.html").exists() },
                 { assert snapshot(path("$outputDir/input/Samplesheet_novaseq.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/pacbio_its.nf.test b/tests/pipeline/pacbio_its.nf.test
@@ -52,7 +52,8 @@ nextflow_pipeline {
                                 path("$outputDir/SBDI/emof.tsv"),
                                 path("$outputDir/SBDI/event.tsv")).match("SBDI") },
                 { assert new File("$outputDir/SBDI/annotation.tsv").exists() },
-                { assert new File("$outputDir/SBDI/asv-table.tsv").exists() }
+                { assert new File("$outputDir/SBDI/asv-table.tsv").exists() },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/pplace.nf.test b/tests/pipeline/pplace.nf.test
@@ -55,7 +55,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/pplace/test_pplace.taxonomy.per_query.tsv").exists() },
                 { assert new File("$outputDir/pplace/test_pplace.graft.test_pplace.epa_result.newick").exists() },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/reftaxcustom.nf.test b/tests/pipeline/reftaxcustom.nf.test
@@ -43,7 +43,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/input/Samplesheet.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/single.nf.test b/tests/pipeline/single.nf.test
@@ -44,7 +44,8 @@ nextflow_pipeline {
                 { assert snapshot(path("$outputDir/input/Samplesheet_single_end.tsv")).match("input") },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"),
                                 path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/sintax.nf.test b/tests/pipeline/sintax.nf.test
@@ -65,7 +65,8 @@ nextflow_pipeline {
                 { assert new File("$outputDir/sintax/ASV_tax_sintax.unite-fungi.tsv").exists() },
                 { assert new File("$outputDir/sintax/ref_taxonomy_sintax.txt").exists() },
                 { assert snapshot(path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"),
-                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") }
+                                path("$outputDir/multiqc/multiqc_data/multiqc_cutadapt.txt")).match("multiqc") },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }

diff --git a/tests/pipeline/test.nf.test b/tests/pipeline/test.nf.test
@@ -93,7 +93,8 @@ nextflow_pipeline {
                                 path("$outputDir/SBDI/emof.tsv"),
                                 path("$outputDir/SBDI/event.tsv")).match("SBDI") },
                 { assert new File("$outputDir/SBDI/annotation.tsv").exists() },
-                { assert new File("$outputDir/SBDI/asv-table.tsv").exists() }
+                { assert new File("$outputDir/SBDI/asv-table.tsv").exists() },
+                { assert new File("$outputDir/summary_report/summary_report.html").exists() }
             )
         }
     }