removing samtools from test, and ignoring geno, ind

Author: jbv2

tests/test_humanpopgen.nf.test

@@ -71,7 +71,7 @@ nextflow_pipeline {
             def stable_name_authentication      = getAllFilesFromDir("$outputDir/authentication"    , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: unstable_patterns_auth)
 
             // Damage manipulation
-            def stable_content_damage_manipulation   = getAllFilesFromDir("$outputDir/damage_manipulation"    , includeDir: false         , ignore: unstable_patterns_auth , ignoreFile: null            , include: ['*', '**/*'] )
+            def stable_content_damage_manipulation   = getAllFilesFromDir("$outputDir/damage_manipulation"    , includeDir: false         , ignore: ['**/*.{bam,bai}'] , ignoreFile: null            , include: ['*', '**/*'] )
             def stable_name_damage_manipulation      = getAllFilesFromDir("$outputDir/damage_manipulation"    , includeDir: false         , ignore: null                   , ignoreFile: null            , include: ['**/*.{bam,bai}'] )
 
             // Deduplication - TODO -> snapshot both lists are empty!?
@@ -83,8 +83,8 @@ nextflow_pipeline {
             def stable_name_final_bams          = getAllFilesFromDir("$outputDir/final_bams"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{bam,bai}'] )
 
             // Genotyping
-            def stable_content_genotyping       = getAllFilesFromDir("$outputDir/genotyping"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*'] )
-            def stable_name_genotyping          = getAllFilesFromDir("$outputDir/genotyping"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.tbi'] )
+            def stable_content_genotyping       = getAllFilesFromDir("$outputDir/genotyping"        , includeDir: false         , ignore: ['**/*.{geno,ind,snp,tsv}']                   , ignoreFile: null                 , include: ['**/*'] )
+            def stable_name_genotyping          = getAllFilesFromDir("$outputDir/genotyping"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{geno,ind,snp,tsv}'] )
 
             // Mapping (incl. bam_input flasgstat)
             def stable_content_mapping          = getAllFilesFromDir("$outputDir/mapping"           , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.flagstat']  )
@@ -103,10 +103,6 @@ nextflow_pipeline {
             def stable_content_readfiltering    = getAllFilesFromDir("$outputDir/read_filtering"    , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.flagstat']  )
             def stable_name_readfiltering       = getAllFilesFromDir("$outputDir/read_filtering"    , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{bam,bai}'] )
 
-            // Samtools
-            def stable_content_samtools   = getAllFilesFromDir("$outputDir/samtools"    , includeDir: false         , ignore: unstable_patterns_auth , ignoreFile: null            , include: ['*', '**/*'] )
-            def stable_name_samtools      = getAllFilesFromDir("$outputDir/samtools"    , includeDir: false         , ignore: null                   , ignoreFile: null            , include: ['**/*.{bam,bai}'] )
-
             // MultiQC
             def stable_name_multiqc             = getAllFilesFromDir("$outputDir/multiqc"           , includeDir: false         , ignore: null                    , ignoreFile: null                , include: ['*', '**/*'] )
 
@@ -133,7 +129,6 @@ nextflow_pipeline {
                 { assert snapshot( stable_content_metagenomics          , stable_name_metagenomics*.name           ).match("metagenomics") },
                 { assert snapshot( stable_content_preprocessing         , stable_name_preprocessing*.name          ).match("preprocessing") },
                 { assert snapshot( stable_content_readfiltering         , stable_name_readfiltering*.name          ).match("read_filtering") },
-                { assert snapshot( stable_content_samtools              , stable_name_samtools*.name               ).match("samtools") },
                 { assert snapshot( stable_name_multiqc*.name ).match("multiqc") },
 
                 // Versions

tests/test_humanpopgen.nf.test.snap

@@ -302,28 +302,25 @@
     "genotyping": {
         "content": [
             [
-                "pileupcaller_genotypes_hs37d5_chr21-MT.geno:md5,242578419851a5778619d3b3b31e2f73",
-                "pileupcaller_genotypes_hs37d5_chr21-MT.ind:md5,15eaec5196fdd95b4914a3714464b721",
-                "pileupcaller_genotypes_hs37d5_chr21-MT.snp:md5,c100677fddc9dafe928c5b0a85621c72",
-                "pileupcaller_genotypes_hs37d5_chr21-MT_coverage.tsv:md5,6b3362405ca6ab80306d7bf658918d4d"
+                
             ],
             [
-                
+                "pileupcaller_genotypes_hs37d5_chr21-MT.geno",
+                "pileupcaller_genotypes_hs37d5_chr21-MT.ind",
+                "pileupcaller_genotypes_hs37d5_chr21-MT.snp",
+                "pileupcaller_genotypes_hs37d5_chr21-MT_coverage.tsv"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "25.04.0"
         },
-        "timestamp": "2025-05-23T10:23:08.46738"
+        "timestamp": "2025-05-23T11:48:39.954805"
     },
     "damage_manipulation": {
         "content": [
             [
-                "JK2067_JK2067_hs37d5_chr21-MT_trimmed.bam:md5,e4b0a68714ed18e46c2cfe812cdae7aa",
-                "JK2067_JK2067_hs37d5_chr21-MT_trimmed.bam.bai:md5,877d54dca22c55dae49f727ef835aed4",
-                "JK2067_downsampled_JK2067_downsampled_hs37d5_chr21-MT_trimmed.bam:md5,0ede97d89412001b9e3d575f21478b77",
-                "JK2067_downsampled_JK2067_downsampled_hs37d5_chr21-MT_trimmed.bam.bai:md5,b7ff326b850a8d3c58c342a5ef48ae58"
+                
             ],
             [
                 "JK2067_JK2067_hs37d5_chr21-MT_trimmed.bam",
@@ -336,7 +333,7 @@
             "nf-test": "0.8.4",
             "nextflow": "25.04.0"
         },
-        "timestamp": "2025-05-23T10:46:43.00917"
+        "timestamp": "2025-05-23T11:48:39.584699"
     },
     "final_bams": {
         "content": [