Fix bug with workflow output index file (#6328)

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

docs/workflow.md

@@ -588,7 +588,7 @@ workflow {
     ch_samples = channel.of(
         [id: 1, name: 'sample 1', fastq_1: '1a.fastq', fastq_2: '1b.fastq'],
         [id: 2, name: 'sample 2', fastq_1: '2a.fastq', fastq_2: '2b.fastq'],
-        [id: 3, name: 'sample 3', fastq_1: '3a.fastq', fastq_2: '3b.fastq']
+        [id: 3, name: 'sample 3', fastq_1: '3a.fastq', fastq_2: null]
     )
 
     publish:
@@ -610,7 +610,7 @@ The above example will write the following CSV file to `results/samples.csv`:
 ```
 "1","sample 1","results/fastq/1a.fastq","results/fastq/1b.fastq"
 "2","sample 2","results/fastq/2a.fastq","results/fastq/2b.fastq"
-"3","sample 3","results/fastq/3a.fastq","results/fastq/3b.fastq"
+"3","sample 3","results/fastq/3a.fastq",""
 ```
 
 You can customize the index file with additional directives, for example:
@@ -629,7 +629,7 @@ This example will produce the following index file:
 "id"|"name"|"fastq_1"|"fastq_2"
 "1"|"sample 1"|"results/fastq/1a.fastq"|"results/fastq/1b.fastq"
 "2"|"sample 2"|"results/fastq/2a.fastq"|"results/fastq/2b.fastq"
-"3"|"sample 3"|"results/fastq/3a.fastq"|"results/fastq/3b.fastq"
+"3"|"sample 3"|"results/fastq/3a.fastq"|""
 ```
 
 :::{note}

modules/nextflow/src/main/groovy/nextflow/extension/PublishOp.groovy

@@ -276,17 +276,15 @@ class PublishOp {
         }
 
         if( value instanceof Map ) {
-            return value
-                .findAll { k, v -> v != null }
-                .collectEntries { k, v ->
-                    if( v instanceof Path )
-                        return Map.entry(k, normalizePath(v, targetResolver))
-                    if( v instanceof Collection<Path> )
-                        return Map.entry(k, normalizePaths(v, targetResolver))
-                    if( v instanceof Map )
-                        return Map.entry(k, normalizePaths(v, targetResolver))
-                    return Map.entry(k, v)
-                }
+            return value.collectEntries { k, v ->
+                if( v instanceof Path )
+                    return Map.entry(k, normalizePath(v, targetResolver))
+                if( v instanceof Collection<Path> )
+                    return Map.entry(k, normalizePaths(v, targetResolver))
+                if( v instanceof Map )
+                    return Map.entry(k, normalizePaths(v, targetResolver))
+                return [k, v]
+            }
         }
 
         throw new IllegalArgumentException("Index file record must be a list, map, or file: ${value} [${value.class.simpleName}]")

modules/nextflow/src/main/groovy/nextflow/script/OutputDsl.groovy

@@ -190,6 +190,10 @@ class OutputDsl {
             setOption('header', value)
         }
 
+        void header(String... value) {
+            setOption('header', value as List)
+        }
+
         void path(String value) {
             setOption('path', value)
         }

modules/nextflow/src/main/groovy/nextflow/util/CsvWriter.groovy

@@ -46,6 +46,9 @@ class CsvWriter {
         else if( header instanceof List ) {
             columns = header
         }
+        else {
+            columns = null
+        }
 
         path.delete()
 

modules/nextflow/src/test/groovy/nextflow/util/CsvWriterTest.groovy

@@ -0,0 +1,41 @@
+package nextflow.util
+
+import spock.lang.Specification
+import test.TestHelper
+/**
+ *
+ * @author Ben Sherman <[email protected]>
+ */
+class CsvWriterTest extends Specification {
+
+    def 'should write csv file'() {
+        given:
+        def file = TestHelper.createInMemTempFile()
+        and:
+        def records = [
+            [id: 1, fastq_1: '1_1.fastq', fastq_2: '1_2.fastq'],
+            [id: 2, fastq_1: '2_1.fastq', fastq_2: '2_2.fastq'],
+            [id: 3, fastq_1: '3_1.fastq', fastq_2: null],
+        ]
+
+        when:
+        new CsvWriter([:]).apply(records, file)
+        then:
+        file.text == '''\
+            "1","1_1.fastq","1_2.fastq"
+            "2","2_1.fastq","2_2.fastq"
+            "3","3_1.fastq",""
+            '''.stripIndent()
+
+        when:
+        new CsvWriter([header: true]).apply(records, file)
+        then:
+        file.text == '''\
+            "id","fastq_1","fastq_2"
+            "1","1_1.fastq","1_2.fastq"
+            "2","2_1.fastq","2_2.fastq"
+            "3","3_1.fastq",""
+            '''.stripIndent()
+    }
+
+}

modules/nf-lang/src/main/java/nextflow/script/dsl/OutputDsl.java

@@ -105,11 +105,6 @@ interface IndexDsl extends DslScope {
         /* List<String> | Boolean */
         void header(Object value);
 
-        @Description("""
-            Closure which defines how to transform each published value into a CSV record. The closure should return a list or map. By default, no transformation is applied.
-        """)
-        void mapper(Closure value);
-
         @Description("""
             The name of the index file relative to the target path (required).
         """)