updated tests

subworkflows/local/input_check.nf

@@ -23,32 +23,33 @@ workflow INPUT_CHECK {
         skip_duplicate_check: true).map {
             // Create grouping value
             meta ->
+
                 // Remove any unallowed charactars in the meta.id field
-                meta[0].id = meta[0].id.replaceAll(/[^A-Za-z0-9_.\-]/, '_')
+                meta[0].id = meta[0].id.replaceAll(/[^A-Za-z0-9_\-]/, '_')
 
                 if (meta[0].external_id != null) {
                     // remove any charactars in the external_id that should not be used
-                    meta[0].id = meta[0].external_id.replaceAll(/[^A-Za-z0-9_.\-]/, '_')
+                    meta[0].id = meta[0].external_id.replaceAll(/[^A-Za-z0-9_\-]/, '_')
                 }else{
                     meta[0].external_id = meta[0].id
                 }
 
 
-                if(processedIDs.contains(meta.id) && params.skip_read_merging){
+                if(processedIDs.contains(meta[0].id) && params.skip_read_merging){
                     // If the id is already contained and read merging is not to be
                     // performed, then we make the id's unique to proceed with processing
                     // read merging is set to false by default, so that when it is run
                     // in IRIDANext reads are only merged in irida next
-                    while (processedIDs.contains(meta.id)) {
-                        meta.id = "${meta.id}_${meta.external_id}"
+                    while (processedIDs.contains(meta[0].id)) {
+                        meta[0].id = "${meta[0].id}_${meta[0].external_id}"
                     }
                 }else{
                     // Set the external id to the input ID.
                     meta[0].external_id = meta[0].id
                 }
 
 
-                processedIDs << meta.id
+                processedIDs << meta[0].id
                 tuple(meta[0].id, meta[0])
         }
 

tests/data/samplesheets/samplesheet-make-names-unique.csv

@@ -0,0 +1,5 @@
+sample,fastq_1,fastq_2,long_reads,assembly
+ha,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/campy-staph1.fq.gz,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/campy-staph2.fq.gz,,
+ha,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/1_R1.fq.gz,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/1_R2.fq.gz,,
+ha,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/metagenomic_reads1.fq.gz,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/metagenomic_reads2.fq.gz,,
+ha,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads.fastq,https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/reads/1_R2.fq,,

tests/subworkflows/local/input_check/input_check.nf.test

@@ -99,14 +99,52 @@ nextflow_workflow {
 
         then {
 
-            // TODO beef up assertions
             assert workflow.success
-            println workflow.out.reads
-            //assert workflow.out.reads[0][0].id == "better_faster_stronger_name"
+            assert workflow.out.reads[0][0].id == 'an_even_stronger_name_'
+            assert workflow.out.reads[0][0].merge == false
+            assert workflow.out.reads[1][0].id == 'better_faster_stronger_name'
+            assert workflow.out.reads[1][0].merge == false
+            assert workflow.out.reads[2][0].id == 'this_is_getting_ridiculous'
+            assert workflow.out.reads[2][0].merge == true
+            assert workflow.out.reads[2][1][0].endsWith("this_is_getting_ridiculous_R1.merged.fastq.gz")
+            assert workflow.out.reads[2][1][1].endsWith("this_is_getting_ridiculous_R2.merged.fastq.gz")
+        }
+
+    }
+
+    test("Test make ids unique") {
+    tag "pass_make_ids_unique"
+
+        when {
+
+            params {
+                input = "$baseDir/tests/data/samplesheets/samplesheet-make-names-unique.csv"
+                outdir = "results"
+                min_reads = 1
+                mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy-staph-ecoli.msh"
+                mh_min_kmer = 1
+                skip_read_merging = true
+                dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
+
+                kraken2_db = "$baseDir/tests/data/kraken2/test"
+
+
+                max_memory = "2.GB"
+                max_cpus = 1
+            }
+
+        }
+
+        then {
+
+            assert workflow.success
+            assert workflow.out.reads[0][0].id = ha
+            assert workflow.out.reads[1][0].id = ha_ha
+            assert workflow.out.reads[2][0].id = ha_ha_ha
+            assert workflow.out.reads[3][0].id = ha_ha_ha_ha
         }
 
     }
 
-    // TODO add test case for making read ids unique
 
 }