updated tests

CHANGELOG.md

@@ -17,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - RASUSA now used for down sampling of Nanopore or PacBio data. [PR 125](https://github.com/phac-nml/mikrokondo/pull/125)
 
+- Sample names (`sample_name` field) can no longer begin with a period. [PR 125](https://github.com/phac-nml/mikrokondo/pull/125)
+
 ### `Updated`
 
 - Documentation and workflow diagram has been updated. [PR 123](https://github.com/phac-nml/mikrokondo/pull/123)

assets/schema_input.json

@@ -16,8 +16,8 @@
             },
             "sample_name": {
                 "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Optional. Used to override sample when used in tools like IRIDA-Next.",
+                "pattern": "^[^\\.]\\S+$",
+                "errorMessage": "Optional. Used to override sample when used in tools like IRIDA-Next. Input cannot start with period.",
                 "meta": ["id"]
             },
             "fastq_1": {

tests/data/samplesheets/samplesheet-test-from-assemblies-vibrio-stupid-names.csv

@@ -0,0 +1,2 @@
+sample,sample_name,fastq_1,fastq_2,long_reads,assembly
+INX,iridanext_output.,,,,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/fake_contigs/vibrio_cholerae/st_120.fa.gz

tests/pipelines/main.from_assemblies.nf.test

@@ -796,4 +796,66 @@ nextflow_pipeline {
         }
     }
 
+        test("Test Stupid Name in Input Sheet") {
+        tag "from_assemblies_stupidnames"
+
+        when {
+            params {
+                // Need to update with 7 gene when complete
+                input = "$baseDir/tests/data/samplesheets/samplesheet-test-from-assemblies-vibrio-stupid-names.csv"
+                outdir = "results"
+
+                platform = "illumina"
+
+                mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/mash.msh"
+                dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
+                lx_allele_database = "$baseDir/tests/data/databases/locidex_dbs"
+                qt_min_contig_length = 1
+
+                skip_bakta = true
+                skip_mobrecon = true
+                skip_checkm = true
+                skip_raw_read_metrics = true
+                skip_polishing = true
+                skip_mlst = true
+                skip_version_gathering = true
+                skip_staramr = true
+                skip_length_filtering_contigs = true
+
+                skip_subtyping = false
+                skip_allele_calling = false
+                lx_report_max_stop = 100
+                max_memory = "2.GB"
+                max_cpus = 1
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert path("$launchDir/results").exists()
+
+            // Compare IRIDANext json
+            assert path("$launchDir/results/iridanext.output.json").exists()
+            def iridanext_json = path("$launchDir/results/iridanext.output.json").json
+            def iridanext_global = iridanext_json.files.global
+            def iridanext_samples = iridanext_json.files.samples
+            def iridanext_metadata = iridanext_json.metadata.samples
+            def vibrio_metadata = iridanext_metadata.INX
+
+            // Output files
+            assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Json/final_report.json" }.size() == 1
+            assert iridanext_global.findAll { it.path == "FinalReports/Aggregated/Tables/final_report.tsv" }.size() == 1
+
+            assert vibrio_metadata.locidex_db_name == "Vibrio cholerae"
+            assert vibrio_metadata.locidex_db_date == "2024-07-30"
+            assert vibrio_metadata.locidex_db_version == "1.0.0"
+            assert vibrio_metadata.total_loci == 7
+            assert vibrio_metadata.count_loci_found == 6
+            assert vibrio_metadata.count_loci_missing == 1
+
+        }
+    }
+
+
 }