update tests

Author: alpae

nf-tests/.nftignore

@@ -6,3 +6,5 @@ orthologs.tsv.gz
 report.*
 **/*.html
 **/*.hogmap
+RootHOGsFasta/*.fa.gz
+OrthologousGroupsFasta/*.fa.gz

nf-tests/default.nf.test

@@ -40,7 +40,19 @@ nextflow_pipeline {
                 sorted_rows.each { row ->
                     lines.add(header.collect { col -> row[col] ?: '' }.join('\t'))
                 }
-                return [name: file.name, md5: listToMD5(lines)]
+                return [name: file.name, md5: listToMD5(lines), lineCount: lines.size()]
+            }
+            def fixed_line_number_files = getAllFilesFromDir(params.output_folder, include:['RootHOGs.tsv', 'OrthologousGroups.tsv', 'orthologs.tsv.gz', "FastOMA_HOGs.orthoxml", 'hogmap/*.hogmap']).collect { file ->
+                def line_count
+                if (file.name.endsWith('.gz')) {
+                    // Use try-with-resources for proper cleanup
+                    new java.util.zip.GZIPInputStream(file.newInputStream()).withCloseable { gzipStream ->
+                        line_count = gzipStream.readLines().size()
+                    }
+                } else {
+                    line_count = file.readLines().size()
+                }
+                return [name: file.name, lineCount: line_count]
             }
 
             assertAll(
@@ -53,7 +65,12 @@ nextflow_pipeline {
                     // All files with stable contents
                     stable_path,
                     // List of all files with timestamps filtered out
-                    timestamp_files
+                    // does not yet work, as hogmap files have percision issues
+                    // and FastOMA_HOGs is not completely deterministic
+                    // timestamp_files 
+
+                    // files with fixed number of lines
+                    fixed_line_number_files
                 ).match() }
             )
         }

nf-tests/default.nf.test.snap

@@ -44,56 +44,44 @@
                 "stats"
             ],
             [
-                "OG_0000001.fa.gz:md5,0d66f05814d8ae19cfc92e9c524732ec",
-                "OG_0000002.fa.gz:md5,ef9c8f91804962843307a71b115398ca",
-                "OG_0000003.fa.gz:md5,a9a53b274a2ee456e8f42f29f7cdd041",
-                "OG_0000004.fa.gz:md5,ae11efbff2957ec2fd5f26e7043f1044",
-                "OG_0000005.fa.gz:md5,9747e7267109929d902a0cd921b9a4a9",
-                "OG_0000006.fa.gz:md5,cc5b8cfcb48b384c870b39c36182add9",
-                "OG_0000007.fa.gz:md5,ad8c0d95094dd8817fe510e752ae7e89",
-                "OG_0000008.fa.gz:md5,b5de472745972a17a29bdf2f0129d8fa",
-                "OG_0000009.fa.gz:md5,4bad2b524cb84aecdf19b0f93ea8534e",
-                "OG_0000010.fa.gz:md5,d9b8763576656b3e747d5a87de6f74b8",
-                "OG_0000011.fa.gz:md5,443fab9c4961ebfb8187165be27a9577",
-                "OG_0000012.fa.gz:md5,e4b128f477155cd74ff10528d7adc09f",
-                "HOG0000001.fa.gz:md5,0d66f05814d8ae19cfc92e9c524732ec",
-                "HOG0000002.fa.gz:md5,ef9c8f91804962843307a71b115398ca",
-                "HOG0000003.fa.gz:md5,a9a53b274a2ee456e8f42f29f7cdd041",
-                "HOG0000004.fa.gz:md5,ae11efbff2957ec2fd5f26e7043f1044",
-                "HOG0000005.fa.gz:md5,9747e7267109929d902a0cd921b9a4a9",
-                "HOG0000006.fa.gz:md5,cc5b8cfcb48b384c870b39c36182add9",
-                "HOG0000007.fa.gz:md5,ad8c0d95094dd8817fe510e752ae7e89",
-                "HOG0000008.fa.gz:md5,b5de472745972a17a29bdf2f0129d8fa",
-                "HOG0000009.fa.gz:md5,4bad2b524cb84aecdf19b0f93ea8534e",
-                "HOG0000010.fa.gz:md5,d9b8763576656b3e747d5a87de6f74b8",
-                "HOG0000011.fa.gz:md5,443fab9c4961ebfb8187165be27a9577",
-                "HOG0000012.fa.gz:md5,e4b128f477155cd74ff10528d7adc09f",
                 "phylostratigraphy.html:md5,060aafe142edbe56cd004090d695177d",
                 "species_tree_checked.nwk:md5,4c82a2f2ffa72a595aaf2fd3deddeff7"
             ],
             [
                 {
                     "name": "FastOMA_HOGs.orthoxml",
-                    "md5": "ac011cd1d734cae01beee5bcb5cda143"
+                    "lineCount": 162
+                },
+                {
+                    "name": "OrthologousGroups.tsv",
+                    "lineCount": 28
+                },
+                {
+                    "name": "RootHOGs.tsv",
+                    "lineCount": 28
                 },
                 {
                     "name": "AQUAE.fa.hogmap",
-                    "md5": "7a8c848990c9dce91d6c50d48ae1ddd1"
+                    "lineCount": 20
                 },
                 {
                     "name": "CHLTR.fa.hogmap",
-                    "md5": "f81877dc801f04e105dbedabe16c5cc0"
+                    "lineCount": 18
                 },
                 {
                     "name": "MYCGE.fa.hogmap",
-                    "md5": "8715ee4eff99f751ca1d3d90b770574c"
+                    "lineCount": 14
+                },
+                {
+                    "name": "orthologs.tsv.gz",
+                    "lineCount": 18
                 }
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "24.10.5"
         },
-        "timestamp": "2025-10-14T16:11:27.355334"
+        "timestamp": "2025-10-23T12:09:08.301966"
     }
 }