DSL2: Nf test conversion: shortDNA

conf/test_shortdna.config

@@ -29,8 +29,7 @@ params {
     fasta                           = params.pipelines_testdata_base_path + 'eager/reference/Mammoth/Mammoth_MT_Krause.fasta'
 
     // Mapping
-    // TO DO: Change when mapAD is there.
-    mapping_tool                    = 'mapad'
+    mapping_tool                       = 'mapad'
 
     // Metagenomics
     run_metagenomics                   = true

tests/shortdna.nf.test

@@ -0,0 +1,141 @@
+nextflow_pipeline {
+
+    name "Test pipeline: NFCORE_EAGER"
+    script "main.nf"
+    tag "pipeline"
+    tag "nfcore_eager"
+    tag "test_shortdna"
+
+    test("test_shortdna_profile") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        then {
+
+            ///////////////////
+            // DOCUMENTATION //
+            ///////////////////
+
+            // The contents of each top level results directory should be tested with individually named snapshots.
+            // Within each snapshot, there should be two to three distinct variables, that contain the files to be tested.
+            //    - stable_name_<dir> is for files with variable md5sums (i.e. content) so only names will be compared
+            //    - stable_content_<dir> is for files with stable md5sums (i.e. content) so md5sums will be compared
+            //    - bams_<dir> is for BAM files, where the headerMD5 is checked for stability (since the content can be unstable)
+            // If a directory is fully stable, you can drop `stable_name_*`
+            // If a directory contains no BAMs, you can drop `bams_*`
+
+            // Generate with: nf-test test --tag test --profile docker,test --update-snapshot
+            // Test with:     nf-test test --tag test --profile docker,test
+            // NOTE: BAMs are always only stable in name, because:
+            //   a) sharding breaks header since the shard that was first is named in the header (Fixed in https://github.com/nf-core/eager/pull/1112)
+            //   b) the order of the reads in the BAMs is not stable (sorted, but reads that share a start position can be in any order)
+            //   point b) also causes BAIs to be unstable.
+            //   c) Merging of multiple BAMs with duplicate @RG / @PG tags can cause the header to be unstable (particularly in the case of shards/lanes)
+
+            //////////////////////
+            // DEFINE VARIABLES //
+            //////////////////////
+
+            // Define exclusion patterns for files with unstable contents
+            // NOTE: When a section needs more than a couple of small patterns, consider adding a variable to store the patterns here
+            //       This is particularly important if the patterns excluded in the stable content section should be included in the stable name section
+            def unstable_patterns_auth = [
+                '**/mapped_reads_gc-content_distribution.txt',
+                '**/mapped_reads_nucleotide_content.txt',
+                '**/genome_gc_content_per_window.png',
+                '**/*.{svg,pdf,html,png,json}',
+                '**/DamageProfiler.log',
+                '**/{3,5}p_freq_misincorporations.txt',
+                '**/DNA_comp_genome.txt',
+                '**/DNA_composition_sample.txt',
+                '**/misincorporation.txt',
+                '**/genome_results.txt',
+                '**/3pGtoA_freq.txt',
+                '**/5pCtoT_freq.txt',
+                '**/lgdistribution.txt',
+                '**/*c_curve.txt',
+                "**/coverage_across_reference.txt",
+                "**/coverage_histogram.txt",
+                "**/duplication_rate_histogram.txt",
+                "**/genome_fraction_coverage.txt",
+                "**/mapping_quality_across_reference.txt",
+                "**/mapping_quality_histogram.txt",
+                ]
+
+            // Check that no files are missing/added
+            // Command legend:                                       Result directory to index      , includeDir: include dirs?, ignore: exclude patterns       , ignoreFile: exclude pattern list , include: include patterns
+            def stable_name_all                 = getAllFilesFromDir("$outputDir/"                  , includeDir: false         , ignore: ['pipeline_info/*']    , ignoreFile: null                 , include: ['*', '**/*'] )
+
+            // Authentication
+            def stable_content_authentication   = getAllFilesFromDir("$outputDir/authentication"    , includeDir: false         , ignore: unstable_patterns_auth , ignoreFile: null                 , include: ['*', '**/*'] )
+            def stable_name_authentication      = getAllFilesFromDir("$outputDir/authentication"    , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: unstable_patterns_auth)
+
+            // Deduplication
+            // NOTE: even the flagstats are unstable, so we only check the names
+            def stable_name_deduplication       = getAllFilesFromDir("$outputDir/deduplication"     , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*'] )
+
+            // Final_bams
+            // NOTE: BAMs are unstable, since upstream BAMs are unstable.
+            def stable_name_final_bams          = getAllFilesFromDir("$outputDir/final_bams"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*'] )
+
+            // Mapping (incl. bam_input flasgstat)
+            def stable_content_mapping          = getAllFilesFromDir("$outputDir/mapping"           , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.flagstat']  )
+            def stable_name_mapping             = getAllFilesFromDir("$outputDir/mapping"           , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{bam,bai}'] )
+
+            // Preprocessing
+            // NOTE: FastQC html appears stable, but I worry it might just include a day timestamp instead of a full timestamp. To keep the expression simpler I removed both from checksum testing.
+            def stable_content_preprocessing    = getAllFilesFromDir("$outputDir/preprocessing"     , includeDir: false         , ignore: ['**/*.{zip,log,html}'], ignoreFile: null                 , include: ['**/*'] )
+            def stable_name_preprocessing       = getAllFilesFromDir("$outputDir/preprocessing"     , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.{zip,log,html}'] )
+
+            // Genotyping
+            // NOTE: single file is created, with unstable content due to unstable BAM input.
+            def stable_name_genotyping          = getAllFilesFromDir("$outputDir/genotyping"        , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['**/*.glf.gz'] )
+
+            // Metagenomics
+            def unstable_patterns_meta = [ // contain the creation date
+                '**/*.{biom,log,megan,rma6}',
+                '**/*table.tsv',
+                '**/log.txt'
+            ]
+
+            def stable_content_metagenomics    = getAllFilesFromDir("$outputDir/metagenomics"       , includeDir: false         , ignore: unstable_patterns_meta , ignoreFile: null                 , include: ['**/*'] )
+            def stable_name_metagenomics       = getAllFilesFromDir("$outputDir/metagenomics"       , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: unstable_patterns_meta )
+
+            // MultiQC
+            def stable_name_multiqc             = getAllFilesFromDir("$outputDir/multiqc"           , includeDir: false         , ignore: null                   , ignoreFile: null                 , include: ['*', '**/*'] )
+
+            ///////////////////////
+            // DEFINE ASSERTIONS //
+            ///////////////////////
+
+            assertAll(
+                { assert workflow.success },
+                // This checks that there are no missing or additional output files.
+                // Also a good starting point to look at all the files in the output folder than need to be checked in subsequent sections.
+                { assert snapshot( stable_name_all*.name             ).match("all_files") },
+
+                // Checking changes to contents of each section
+                // NOTE: Keep the order of the sections in the alphanumeric order of the output directories.
+                //    Each section should first check stable_content, stable_name second (if applicable).
+                { assert snapshot( stable_content_authentication     , stable_name_authentication*.name   ).match("authentication") },
+                { assert snapshot(                                     stable_name_deduplication*.name    ).match("deduplication") },
+                { assert snapshot(                                     stable_name_final_bams*.name       ).match("final_bams") },
+                // NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279
+                { assert snapshot( stable_content_mapping            , stable_name_mapping*.name          ).match("mapping_output") },
+                { 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_name_genotyping*.name       ).match("genotyping") },
+                { assert snapshot( stable_content_metagenomics       , stable_name_metagenomics*.name     ).match("metagenomics") },
+                { assert snapshot( stable_name_multiqc*.name         ).match("multiqc") },
+
+                // Versions
+                { assert new File("$outputDir/pipeline_info/nf_core_eager_software_mqc_versions.yml").exists() },
+
+            )
+        }
+    }
+}