fix(tests): remove unstable files from affy test snapshots

nf-core · Feb 4, 2025 · 80bda7b · 80bda7b
1 parent 278b88f
commit 80bda7b
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Showing 8 changed files with 14 additions and 17 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -5,11 +5,12 @@ report/gsea/**/*butterfly_plot.png
 report/gsea/**/*.gsea_report_for_hND6.tsv
 report/gsea/**/*.symbols.Gsea.rpt
 report/gsea/**/*.html
-report/gsea/phenotype_uninvolved_lesional/**/*.png
-report/gsea/**/phenotype_uninvolved_lesional.*.gsea_report_for_*.tsv
+report/gsea/phenotype_uninvolved_lesional_GSE50790/**/*.png
+report/gsea/**/phenotype_uninvolved_lesional_GSE50790.*.gsea_report_for_*.tsv
 report/*.html
 report/*.zip
 *html
 shinyngs_app/**/data.rds
-report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.{html,tsv}
-report/gsea/phenotype_uninvolved_lesional/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.{html,tsv}
+report/gsea/phenotype_uninvolved_lesional_GSE50790/h.all.v2022.1.Hs.symbols/gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.{html,tsv}
+report/gsea/phenotype_uninvolved_lesional_GSE50790/h.all.v2022.1.Hs.symbols/gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.{html,tsv}
+**/*.png
diff --git a/tests/test.nf.test b/tests/test.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
             // 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', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

diff --git a/tests/test_affy.nf.test b/tests/test_affy.nf.test
@@ -17,11 +17,10 @@ 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}',
-                    'report/gsea/phenotype_uninvolved_lesional_GSE50790/**/*.png',
-                    'report/gsea/phenotype_uninvolved_lesional_GSE50790/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_GLYCOLYSIS.{html,tsv}',
-                    'report/gsea/phenotype_uninvolved_lesional_GSE50790/h.all.v2022.1.Hs.symbols/phenotype_uninvolved_lesional.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.{html,tsv}'])
+                    'report/gsea/phenotype_uninvolved_lesional_GSE50790/**/*.png'
+            ])
             // stable_path: All files in ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

diff --git a/tests/test_affy.nf.test.snap b/tests/test_affy.nf.test.snap
@@ -204,7 +204,6 @@
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_MYOGENESIS.tsv:md5,332f9386161436cd69d4b830e0f392d6",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_NOTCH_SIGNALING.tsv:md5,53bc5acac191f31dcdbfe62fcf396358",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_OXIDATIVE_PHOSPHORYLATION.tsv:md5,faab3d7cea1ff32b5c224587246ad34e",
-                "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_P53_PATHWAY.tsv:md5,4070abb7bce1b665cae361d1fafadc4a",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_PEROXISOME.tsv:md5,66a120807b07d920c876b65b3925264c",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_PROTEIN_SECRETION.tsv:md5,d13300c61a1e99a0b05ef18fac74c42d",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY.tsv:md5,33429d1e3f2342c6c0e7b499035bd8da",
@@ -215,8 +214,6 @@
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.HALLMARK_WNT_BETA_CATENIN_SIGNALING.tsv:md5,4f11dba4f7cbc92f589bef27c182d91d",
                 "gene_sets_phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.Symbol_to_probe_set_mapping_details.tsv:md5,a619edb7acb1a0208389f7faf35eb30c",
                 "phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.gene_set_sizes.tsv:md5,77b53b0ca686ede9fe15ca448340f9f5",
-                "phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.gsea_report_for_lesional.tsv:md5,dd05ffd4fae9d1b5539d1f74c016ec5d",
-                "phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.gsea_report_for_uninvolved.tsv:md5,b3de35531f650651529c6f53d81ab1da",
                 "phenotype_uninvolved_lesional_GSE50790.h.all.v2022.1.Hs.symbols.ranked_gene_list_lesional_versus_uninvolved.tsv:md5,72dfaeff534ba9a2b32f63524e835dc4",
                 "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
                 "versions.yml:md5,27cf350d1f743e60e64b4434cf6d4687",
@@ -237,6 +234,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-04T16:52:57.326488609"
+        "timestamp": "2025-02-04T17:09:00.489407892"
     }
 }
diff --git a/tests/test_maxquant.nf.test b/tests/test_maxquant.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
             // 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', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

diff --git a/tests/test_nogtf.nf.test b/tests/test_nogtf.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
             // 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', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

diff --git a/tests/test_rnaseq_limma.nf.test b/tests/test_rnaseq_limma.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
             // 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', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

diff --git a/tests/test_soft.nf.test b/tests/test_soft.nf.test
@@ -18,7 +18,7 @@ nextflow_pipeline {
             // 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', ignore: ['**/*.png'])
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(