Add Points2Regions module with clustering and plotting templates

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*

.nf-test.log

@@ -0,0 +1,50 @@
+Mar-25 18:17:56.633 [main] INFO  com.askimed.nf.test.App - nf-test 0.9.2
+Mar-25 18:17:56.639 [main] INFO  com.askimed.nf.test.App - Arguments: [test, modules/local/points2regions/tests/main.nf.test, --profile, docker]
+Mar-25 18:17:57.026 [main] INFO  com.askimed.nf.test.App - Nextflow Version: 24.10.5
+Mar-25 18:17:57.028 [main] WARN  com.askimed.nf.test.commands.RunTestsCommand - No nf-test config file found.
+Mar-25 18:17:57.058 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Loaded 43 files from directory /Users/obrovkina/Documents/Projects/spatialxe in 0.029 sec
+Mar-25 18:17:57.059 [main] INFO  com.askimed.nf.test.lang.dependencies.DependencyResolver - Found 1 files containing tests.
+Mar-25 18:17:57.059 [main] DEBUG com.askimed.nf.test.lang.dependencies.DependencyResolver - Found files: [/Users/obrovkina/Documents/Projects/spatialxe/modules/local/points2regions/tests/main.nf.test]
+Mar-25 18:17:57.280 [main] INFO  com.askimed.nf.test.commands.RunTestsCommand - Found 1 tests to execute.
+Mar-25 18:17:57.280 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Started test plan
+Mar-25 18:17:57.280 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Running testsuite 'Test Process POINTS2REGIONS_CLUSTER' from file '/Users/obrovkina/Documents/Projects/spatialxe/modules/local/points2regions/tests/main.nf.test'.
+Mar-25 18:17:57.280 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Run test '9b856baf: cluster - with Xenium transcripts.csv'. type: com.askimed.nf.test.lang.process.ProcessTest
+Mar-25 18:18:11.859 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Test '9b856baf: cluster - with Xenium transcripts.csv' finished. status: FAILED
+org.codehaus.groovy.runtime.powerassert.PowerAssertionError: 2 of 2 assertions failed
+	at com.askimed.nf.test.lang.extensions.GlobalMethods.assertAll(GlobalMethods.java:48)
+	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.invoke(StaticMetaMethodSite.java:44)
+	at org.codehaus.groovy.runtime.callsite.StaticMetaMethodSite.callStatic(StaticMetaMethodSite.java:100)
+	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallStatic(CallSiteArray.java:55)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:217)
+	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callStatic(AbstractCallSite.java:240)
+	at main_nf$_run_closure1$_closure3$_closure7.doCall(main.nf.test:33)
+	at main_nf$_run_closure1$_closure3$_closure7.doCall(main.nf.test)
+	at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103)
+	at java.base/java.lang.reflect.Method.invoke(Method.java:580)
+	at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
+	at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
+	at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
+	at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1030)
+	at groovy.lang.Closure.call(Closure.java:427)
+	at groovy.lang.Closure.call(Closure.java:406)
+	at com.askimed.nf.test.lang.TestCode.execute(TestCode.java:16)
+	at com.askimed.nf.test.lang.process.ProcessTest.execute(ProcessTest.java:171)
+	at com.askimed.nf.test.core.TestExecutionEngine.execute(TestExecutionEngine.java:165)
+	at com.askimed.nf.test.commands.RunTestsCommand.execute(RunTestsCommand.java:298)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:43)
+	at com.askimed.nf.test.commands.AbstractCommand.call(AbstractCommand.java:18)
+	at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
+	at picocli.CommandLine.access$1300(CommandLine.java:145)
+	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
+	at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
+	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
+	at picocli.CommandLine.execute(CommandLine.java:2078)
+	at com.askimed.nf.test.App.run(App.java:39)
+	at com.askimed.nf.test.App.main(App.java:46)
+Mar-25 18:18:11.860 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Testsuite 'Test Process POINTS2REGIONS_CLUSTER' finished. snapshot file: false, skipped tests: false, failed tests: true
+Mar-25 18:18:11.860 [main] INFO  com.askimed.nf.test.core.TestExecutionEngine - Executed 1 tests. 1 tests failed. Done!

.nf-test/tests/9b856baf5b74f66fed52051240a30667/meta/mock.nf

@@ -0,0 +1,97 @@
+import groovy.json.JsonGenerator
+import groovy.json.JsonGenerator.Converter
+
+nextflow.enable.dsl=2
+
+// comes from nf-test to store json files
+params.nf_test_output  = ""
+
+// include dependencies
+
+include { UNZIP  } from '/Users/obrovkina/Documents/Projects/spatialxe/modules/nf-core/unzip/main.nf'
+
+
+// include test process
+include { POINTS2REGIONS_CLUSTER } from '/Users/obrovkina/Documents/Projects/spatialxe/modules/local/points2regions/tests/../main.nf'
+
+// define custom rules for JSON that will be generated.
+def jsonOutput =
+    new JsonGenerator.Options()
+        .addConverter(Path) { value -> value.toAbsolutePath().toString() } // Custom converter for Path. Only filename
+        .build()
+
+def jsonWorkflowOutput = new JsonGenerator.Options().excludeNulls().build()
+
+
+workflow {
+
+    // run dependencies
+
+    {
+        def input = []
+
+                input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)]
+
+        UNZIP(*input)
+    }
+
+
+    // process mapping
+    def input = []
+
+                input[0] = Channel.of([
+                        [id: "test"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] }  + "/transcripts.csv")
+                input[1] = 20
+                input[2] = 5
+
+    //----
+
+    //run process
+    POINTS2REGIONS_CLUSTER(*input)
+
+    if (POINTS2REGIONS_CLUSTER.output){
+
+        // consumes all named output channels and stores items in a json file
+        for (def name in POINTS2REGIONS_CLUSTER.out.getNames()) {
+            serializeChannel(name, POINTS2REGIONS_CLUSTER.out.getProperty(name), jsonOutput)
+        }	  
+
+        // consumes all unnamed output channels and stores items in a json file
+        def array = POINTS2REGIONS_CLUSTER.out as Object[]
+        for (def i = 0; i < array.length ; i++) {
+            serializeChannel(i, array[i], jsonOutput)
+        }    	
+
+    }
+
+}
+
+def serializeChannel(name, channel, jsonOutput) {
+    def _name = name
+    def list = [ ]
+    channel.subscribe(
+        onNext: {
+            list.add(it)
+        },
+        onComplete: {
+              def map = new HashMap()
+              map[_name] = list
+              def filename = "${params.nf_test_output}/output_${_name}.json"
+              new File(filename).text = jsonOutput.toJson(map)		  		
+        } 
+    )
+}
+
+
+workflow.onComplete {
+
+    def result = [
+        success: workflow.success,
+        exitStatus: workflow.exitStatus,
+        errorMessage: workflow.errorMessage,
+        errorReport: workflow.errorReport
+    ]
+    new File("${params.nf_test_output}/workflow.json").text = jsonWorkflowOutput.toJson(result)
+
+}