Add topics

Author: famosab

workflows/vcftomaf/main.nf

@@ -40,8 +40,8 @@ workflow VCFTOMAF {
 
     main:
 
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
 
     //
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
@@ -121,20 +121,43 @@ workflow VCFTOMAF {
     //
     // Collate and save software versions
     //
-    softwareVersionsToYAML(ch_versions)
-        .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_pipeline_software_mqc_versions.yml', sort: true, newLine: true)
+    def topic_versions = channel.topic("versions")
+        .distinct()
+        .branch { entry ->
+            versions_file: entry instanceof Path
+            versions_tuple: true
+        }
+
+    def topic_versions_string = topic_versions.versions_tuple
+        .map { process, tool, version ->
+            [process[process.lastIndexOf(':') + 1..-1], "  ${tool}: ${version}"]
+        }
+        .groupTuple(by: 0)
+        .map { process, tool_versions ->
+            tool_versions.unique().sort()
+            "${process}:\n${tool_versions.join('\n')}"
+        }
+
+    softwareVersionsToYAML(ch_versions.mix(topic_versions.versions_file))
+        .mix(topic_versions_string)
+        .collectFile(
+            storeDir: "${params.outdir}/pipeline_info",
+            name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml',
+            sort: true,
+            newLine: true,
+        )
         .set { ch_collated_versions }
 
     //
     // MODULE: MultiQC
     //
-    ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
-    ch_multiqc_logo                       = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
+    ch_multiqc_config                     = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    ch_multiqc_custom_config              = params.multiqc_config ? channel.fromPath(params.multiqc_config, checkIfExists: true) : channel.empty()
+    ch_multiqc_logo                       = params.multiqc_logo ? channel.fromPath(params.multiqc_logo, checkIfExists: true) : channel.empty()
     summary_params                        = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
-    ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(summary_params))
+    ch_workflow_summary                   = channel.value(paramsSummaryMultiqc(summary_params))
     ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
-    ch_methods_description                = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
+    ch_methods_description                = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_collated_versions)
     ch_multiqc_files                      = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: false))