Add test for hash-missing

tests/data/called/expected_results_missing.txt

@@ -0,0 +1,5 @@
+id	address	level_1
+sample1	1	1
+sample2	1	1
+sample3	2	2
+sampleQ	1	1

tests/data/clusters/expected_clusters_missing.txt

@@ -0,0 +1,4 @@
+id	address	level_1
+sample1	1	1
+sample2	1	1
+sample3	2	2

tests/data/distances/expected_dists_missing.txt

@@ -0,0 +1,5 @@
+query_id	ref_id	dist
+sampleQ	sampleQ	0
+sampleQ	sample1	1
+sampleQ	sample2	1
+sampleQ	sample3	2

tests/data/irida/missing_iridanext.output.json

@@ -0,0 +1,17 @@
+{
+    "files": {
+        "global": [
+
+        ],
+        "samples": {
+
+        }
+    },
+    "metadata": {
+        "samples": {
+            "sampleQ": {
+                "address": "1"
+            }
+        }
+    }
+}

tests/data/profiles/expected-profile_missing1.tsv

@@ -0,0 +1,5 @@
+sample_id	l1	l2	l3
+sampleQ	1	2	1
+sample1	1	1	1
+sample2	-	1	1
+sample3	-	1	2

tests/data/profiles/expected-profile_missing2.tsv

@@ -0,0 +1,2 @@
+sample_id	l1	l2	l3
+sampleQ	1	2	1

tests/data/reports/sample2_missing.mlst.json

@@ -0,0 +1,7 @@
+{
+    "sample2": {
+        "l1": "-",
+        "l2": "1",
+        "l3": "1"
+    }
+}

tests/data/reports/sample3_missing.mlst.json

@@ -0,0 +1,7 @@
+{
+    "sample3": {
+        "l1": "-",
+        "l2": "1",
+        "l3": "2"
+    }
+}

tests/data/samplesheets/samplesheet-hash_missing.csv

@@ -0,0 +1,6 @@
+sample,mlst_alleles,address
+sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json,
+sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1
+sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/add_tests/tests/data/reports/sample2_missing.mlst.json,1
+sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/add_tests/tests/data/reports/sample3_missing.mlst.json,2
+

tests/pipelines/main_missing_alleles.nf.test

@@ -0,0 +1,61 @@
+nextflow_pipeline {
+
+    name "Integration Tests for parameters dealing with missing or removed alleles"
+    script "main.nf"
+
+    test("Full pipeline hashes and missing data") {
+        tag "pipeline_hashes_missing"
+
+        when {
+            params {
+                input = "$baseDir/tests/data/samplesheets/samplesheet-hash_missing.csv"
+                outdir = "results"
+
+                gm_thresholds = "1"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert path("$launchDir/results").exists()
+
+            // Check merged profiles
+            def actual_profile_ref = path("$launchDir/results/locidex/merge/reference/merged_ref/merged_profiles_ref.tsv")
+            def expected_profile_tsv = path("$baseDir/tests/data/profiles/expected-profile_missing1.tsv")
+            assert actual_profile_ref.text == expected_profile_tsv.text
+
+            // Check query profiles
+            def actual_profile_query = path("$launchDir/results/locidex/merge/query/merged_value/merged_profiles_value.tsv")
+            def expected_profile_query_tsv = path("$baseDir/tests/data/profiles/expected-profile_missing2.tsv")
+            assert actual_profile_query.text == expected_profile_query_tsv.text
+
+            // Check computed pairwise distances
+            def actual_distances = path("$launchDir/results/distances/results.text")
+            def expected_distances = path("$baseDir/tests/data/distances/expected_dists_missing.txt")
+            assert actual_distances.text == expected_distances.text
+
+            // Verify cluster file
+            def actual_cluster = path("$launchDir/results/cluster/reference_clusters.txt")
+            def expected_cluster = path("$baseDir/tests/data/clusters/expected_clusters_missing.txt")
+            assert actual_cluster.text == expected_cluster.text
+
+            // Check called clusters
+            def actual_calls = path("$launchDir/results/call/Called/results.text")
+            def expected_calls = path("$baseDir/tests/data/called/expected_results_missing.txt")
+            assert actual_calls.text == expected_calls.text
+
+            // Check IRIDA Next JSON output
+            assert path("$launchDir/results/iridanext.output.json").json == path("$baseDir/tests/data/irida/missing_iridanext.output.json").json
+
+            def iridanext_json = path("$launchDir/results/iridanext.output.json").json
+            def iridanext_samples = iridanext_json.files.samples
+            def iridanext_metadata = iridanext_json.metadata.samples
+
+            assert iridanext_metadata.size() == 1 && iridanext_metadata.containsKey("sampleQ")
+            assert iridanext_metadata.sampleQ."address" == "1"
+        }
+    }
+
+
+}
+