Fix wrroc problems

nf-prov-test/main.nf

@@ -37,10 +37,14 @@ process WC_SAMPLE {
     input:
     tuple val(id), path(fastq_1), path(fastq_2)
 
+    output:
+    tuple val(id), path('counts.txt')
+
     script:
     """
-    wc -l ${fastq_1}
-    wc -l ${fastq_2}
+    touch counts.txt
+    wc -l ${fastq_1} >> counts.txt
+    wc -l ${fastq_2} >> counts.txt
     """
 }
 
@@ -53,11 +57,12 @@ workflow {
     ECHO_EXEC(inputs_ch)
 
     samples_ch = channel.fromPath(params.input).splitCsv(header: true)
-    WC_SAMPLE(samples_ch)
+    counts_ch = WC_SAMPLE(samples_ch)
 
     publish:
     script = ECHO_SCRIPT.out
     exec = ECHO_EXEC.out
+    counts = counts_ch
 }
 
 output {
@@ -74,4 +79,8 @@ output {
             path 'exec.json'
         }
     }
+
+    counts {
+        path '.'
+    }
 }

src/main/groovy/nextflow/prov/renderers/WrrocRenderer.groovy

@@ -19,6 +19,7 @@ package nextflow.prov.renderers
 import java.nio.file.FileSystems
 import java.nio.file.Files
 import java.nio.file.Path
+import java.nio.file.Paths
 import java.time.LocalDateTime
 import java.time.format.DateTimeFormatter
 
@@ -91,6 +92,12 @@ class WrrocRenderer implements Renderer {
         final nextflowVersion = metadata.nextflow.version.toString()
         final params = session.params
 
+        // get various pipeline_info configurations
+        final reportOpts = session.config.navigate('report', [:]) as Map
+        final timelineOpts = session.config.navigate('timeline', [:]) as Map
+        final dagOpts = session.config.navigate('dag', [:]) as Map
+        final traceOpts = session.config.navigate('trace', [:]) as Map
+
         // parse wrroc configuration
         final wrrocOpts = session.config.navigate('prov.formats.wrroc', [:]) as Map
         final agent = getAgentInfo(wrrocOpts)
@@ -208,6 +215,51 @@ class WrrocRenderer implements Renderer {
                 ] as Map
             }
 
+        // -- pipeline_info files
+        if(reportOpts.enabled) {
+            Path relativeReportPath = crateDir.relativize(Paths.get(reportOpts.file.toString()))
+            datasetParts.add([
+                "@id"           : relativeReportPath.toString(),
+                "@type"         : "File",
+                "name"          : relativeReportPath.getFileName().toString(),
+                "description"   : "Nextflow execution report",
+                "encodingFormat": "text/html"
+            ])
+        }
+
+        if(timelineOpts.enabled) {
+            Path relativeTimelinePath = crateDir.relativize(Paths.get(timelineOpts.file.toString()))
+            datasetParts.add([
+                "@id"           : relativeTimelinePath.toString(),
+                "@type"         : "File",
+                "name"          : relativeTimelinePath.getFileName().toString(),
+                "description"   : "Nextflow execution timeline",
+                "encodingFormat": "text/html"
+            ])
+        }
+
+        if(dagOpts.enabled) {
+            Path relativeDagPath = crateDir.relativize(Paths.get(dagOpts.file.toString()))
+            datasetParts.add([
+                "@id"           : relativeDagPath.toString(),
+                "@type"         : "File",
+                "name"          : relativeDagPath.getFileName().toString(),
+                "description"   : "Nextflow execution DAG",
+                "encodingFormat": "text/html"
+            ])
+        }
+
+        if(traceOpts.enabled) {
+            Path relativeTracePath = crateDir.relativize(Paths.get(traceOpts.file.toString()))
+            datasetParts.add([
+                "@id"           : relativeTracePath.toString(),
+                "@type"         : "File",
+                "name"          : relativeTracePath.getFileName().toString(),
+                "description"   : "Nextflow execution DAG",
+                "encodingFormat": "text/plain"
+            ])
+        }
+
         // -- input files
         Map<Path,String> paramInputFiles = [:]
 
@@ -347,7 +399,7 @@ class WrrocRenderer implements Renderer {
                 // HACK: when the owner script of a processor defines only one process, that must be the definition
                 final meta = ScriptMeta.get(processor.getOwnerScript())
                 final defs = meta.getDefinitions().findAll { defn -> defn instanceof ProcessDef } as List<ProcessDef>
-                final processDef = defs.size() == 1 ? defs.first() : null
+                final processDef = defs.find { it.name == processor.name }
                 if( !processDef )
                     log.warn "Could not identify process definition for `${processor.name}` -- resulting RO-Crate may be invalid (hint: define each process in a separate module script to fix this issue)"
                 acc[processor] = processDef