add simple support for CSV and TSV

plugins/nf-schema/src/main/nextflow/validation/ValidationExtension.groovy

@@ -110,21 +110,21 @@ class ValidationExtension extends PluginExtensionPoint {
 
     @Function
     public void listToSamplesheet(
-        final List inputList,
+        final List<Map> inputList,
         final CharSequence samplesheet,
         final Object schema = null
     ) {
         def Path samplesheetFile = Nextflow.file(samplesheet) as Path
-        listToSamplesheet(inputList, samplesheetFile, schemaFile)
+        listToSamplesheet(inputList, samplesheetFile, schema)
     }
 
     @Function
     public void listToSamplesheet(
-        final List inputList,
+        final List<Map> inputList,
         final Path samplesheet,
         final Object schema = null
     ) {
-        def Path schemaFile = null
+        def Path schemaFile
         if(schema) {
             if(schema instanceof String) {
                 schemaFile = Nextflow.file(getBasePath(session.baseDir.toString(), schema as String)) as Path

plugins/nf-schema/src/main/nextflow/validation/exceptions/SamplesheetCreationException.groovy

@@ -0,0 +1,16 @@
+package nextflow.validation.exceptions
+
+import groovy.transform.CompileStatic
+import nextflow.exception.AbortOperationException
+/**
+ * Exception thrown to notify issues with the samplesheet creation
+ *
+ * @author Nicolas Vannieuwkerke <[email protected]>
+ */
+@CompileStatic
+class SamplesheetCreationException extends AbortOperationException {
+
+    SamplesheetCreationException(String message) {
+        super(message)
+    }
+}

plugins/nf-schema/src/main/nextflow/validation/samplesheet/ListConverter.groovy

@@ -4,6 +4,8 @@ import groovy.util.logging.Slf4j
 import java.nio.file.Path
 
 import nextflow.validation.config.ValidationConfig
+import nextflow.validation.exceptions.SamplesheetCreationException
+import static nextflow.validation.utils.Files.getFileType
 
 /**
  *
@@ -20,10 +22,67 @@ class ListConverter {
     }
 
     public void validateAndConvertToSamplesheet(
-        List inputList,
+        List<Map> inputList,
         Path samplesheet,
         Path schema
     ) {
-        println("Hi")
+        def String fileType = getFileType(samplesheet)
+        if(["csv", "tsv"].contains(fileType) && isNested(inputList)) {
+            def String msg = "Cannot create a CSV or TSV samplesheet from a list of nested values."
+            throw new SamplesheetCreationException(msg)
+        }
+
+        switch(fileType) {
+            case "csv":
+                createSeparatedValueFile(inputList, samplesheet, ",")
+                break
+            case "tsv":
+                createSeparatedValueFile(inputList, samplesheet, "\t")
+                break
+        }
+    }
+
+    private Boolean isNested(List input) {
+        def Boolean nested = false
+        input.each { entry ->
+            entry.each { key, element ->
+                if(element instanceof List || element instanceof Map) {
+                    nested = true
+                    return
+                }
+            }
+            if(nested) return
+        }
+        return nested
+    }
+
+    private List<String> determineHeader(List<Map> inputList) {
+        def List<String> headers = []
+        inputList.each { entry ->
+            entry.each { key, element ->
+                if(!headers.contains(key)) {
+                    headers.add(key)
+                }
+            }
+        }
+        return headers
+    }
+
+    private void createSeparatedValueFile(List<Map> inputList, Path samplesheet, String delimiter) {
+        def List<String> headers = determineHeader(inputList)
+        def List<String> content = [headers.join(delimiter)]
+        inputList.each { entry ->
+            def List<String> entryContent = []
+            headers.each { header ->
+                def Object item = entry.get(header)
+                if(item == null) {
+                    entryContent.add("")
+                } else {
+                    entryContent.add(item.toString())
+                }
+            }
+            content.add(entryContent.join(delimiter))
+        }
+        samplesheet.text = content.join("\n")
     }
 }

plugins/nf-schema/src/main/nextflow/validation/utils/Files.groovy

@@ -9,6 +9,7 @@ import groovy.json.JsonGenerator
 import groovy.json.JsonSlurper
 import groovy.util.logging.Slf4j
 import java.nio.file.Path
+import java.nio.file.NoSuchFileException
 
 import nextflow.validation.exceptions.SchemaValidationException
 import static nextflow.validation.utils.Common.getValueFromJsonPointer
@@ -34,13 +35,18 @@ public class Files {
             return extension == "yml" ? "yaml" : extension
         }
 
-        def String header = getFileHeader(file)
-
-        def Integer commaCount = header.count(",")
-        def Integer tabCount = header.count("\t")
+        def Integer commaCount = 0
+        def Integer tabCount = 0
+        try {
+            def String header = getFileHeader(file)
+            commaCount = header.count(",")
+            tabCount = header.count("\t")
+        } catch (NoSuchFileException e) {
+            log.debug("${file.toString()} does not exist, cannot infer file type from file content.")
+        }
 
         if ( commaCount == tabCount ){
-            log.error("Could not derive file type from ${file}. Please specify the file extension (CSV, TSV, YML, YAML and JSON are supported).".toString())
+            throw new SchemaValidationException("Could not derive file type from ${file}. Please specify the file extension (CSV, TSV, YML, YAML and JSON are supported).".toString())
         }
         if ( commaCount > tabCount ){
             return "csv"