From 80bda7bb149ce845f05ff8d722425f2002b908e5 Mon Sep 17 00:00:00 2001 From: Suzanne Jin Date: Tue, 4 Feb 2025 17:35:22 +0000 Subject: [PATCH] fix(tests): remove unstable files from affy test snapshots --- tests/.nftignore | 9 +++++---- tests/test.nf.test | 2 +- tests/test_affy.nf.test | 7 +++---- tests/test_affy.nf.test.snap | 5 +---- tests/test_maxquant.nf.test | 2 +- tests/test_nogtf.nf.test | 2 +- tests/test_rnaseq_limma.nf.test | 2 +- tests/test_soft.nf.test | 2 +- 8 files changed, 14 insertions(+), 17 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index cfb2b95c..604f6bbe 100644 --- 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 index df2194a0..0613105c 100644 --- 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 index 2e4bdcd8..4e612ea7 100644 --- 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 index d835f6b5..1cf1e3e2 100644 --- 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" } } \ No newline at end of file diff --git a/tests/test_maxquant.nf.test b/tests/test_maxquant.nf.test index 75c0e08d..a9c7cc7f 100644 --- 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 index efee3f00..263513d2 100644 --- 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 index d04a74f9..5139b177 100644 --- 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 index 5cbffb7f..0d8b6605 100644 --- 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(