Resolved conflicts between dev and update-parameters

modules/local/cluster_file/main.nf

@@ -10,24 +10,33 @@ process CLUSTER_FILE {
 
     exec:
     def outputLines = []
+    def delimiter = java.util.regex.Pattern.quote(params.gm_delimiter)
 
     // Determine the maximum number of levels to set the header requirements for each pipeline run
-    int maxLevels = meta.collect { sample -> sample.address.split("\\.").size() }.max() ?: 0
+    int maxLevels = meta.collect { sample -> sample.address.split(delimiter).size() }.max() ?: 0
 
-    // Generate the header
+    // Verify each sample is consistent with $maxLevels
+    meta.each { sample ->
+        int level = sample.address.split(delimiter).size()
+        if (level != maxLevels) {
+            error ("Inconsistent levels found: expected $maxLevels levels but found $level levels in ${sample.id}")
+        }
+    }
+
+    // Generate the header for the expected_clusters.txt file
     def header = ["id", "address"] + (1..maxLevels).collect { "level_$it" }
     outputLines << header.join("\t")
 
     // Iterate over each sample in the meta list and pull the relevant information for the text file
     meta.each { sample ->
         def id = sample.id
         def address = sample.address
-        def levels = address.split("\\.")
-        def line = [id, address] + levels.collect { it.toString() } + (levels.size()..<maxLevels).collect { "" }
+        def levels = address.split(delimiter)
+        def line = [id, address] + levels.collect { it.toString() }
         outputLines << line.join("\t")
     }
 
-    // Write the text file
+    // Write the text file, iterating over each sample
     task.workDir.resolve("expected_clusters.txt").withWriter { writer ->
         outputLines.each { line ->
             writer.writeLine(line)

tests/data/clusters/expected_clusters.txt

@@ -1,4 +1,4 @@
 id	address	level_1	level_2	level_3
 sample1	1.1.1	1	1	1
 sample2	1.1.1	1	1	1
-sample3	2.2.2	2	2	2
+sample3	1.1.2	1	1	2

tests/data/profiles/expected-profile2.tsv

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

tests/modules/cluster_file/main.nf.test

@@ -0,0 +1,58 @@
+nextflow_process {
+    name "Test Process CLUSTER_FILE"
+    script "modules/local/cluster_file/main.nf"
+    process "CLUSTER_FILE"
+
+    test("Test when sample levels are equal") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [['id':'sample1', 'address':'1.1.1'],
+                    ['id':'sample2', 'address':'1.1.1'],
+                    ['id':'sample3', 'address':'1.1.2']]
+                    )
+                """
+            }
+
+            params {
+                outdir = "cluster_results"
+            }
+        }
+
+        then {
+            assert process.success
+            assert path("$launchDir/cluster_results").exists()
+
+            // Check expected_clusters
+            def actual_clusters = path("$launchDir/cluster_results/cluster/expected_clusters.txt")
+            def expected_clusters = path("$baseDir/tests/data/clusters/expected_clusters.txt")
+            assert actual_clusters.text == expected_clusters.text
+        }
+    }
+
+    test("Test when sample levels are different") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(
+                    [['id':'sample1', 'address':'1.1.1'],
+                    ['id':'sample2', 'address':'1.1.1'],
+                    ['id':'sample3', 'address':'1.2']]
+                    )
+                """
+            }
+
+            params {
+                outdir = "cluster_results"
+            }
+        }
+
+        then {
+            assert process.failed
+            assert (process.stdout =~ /Inconsistent levels found: expected 3 levels but found 2 levels in sample3/).find()
+        }
+    }
+}

tests/pipelines/main.nf.test

@@ -18,11 +18,15 @@ nextflow_pipeline {
             assert path("$launchDir/results").exists()
 
             // Check merged profiles
-            // TODO check query profile is merged
             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-profile1.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-profile2.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_pairwise_dists.txt")