Merge branch 'multiqc' of https://github.com/nf-core/rnafusion into m…

…ultiqc

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Set html files as optional in fusionreport [#380](https://github.com/nf-core/rnafusion/pull/380)
 - Provide gene count file by default when running STAR_FOR_STARFUSION [#385](https://github.com/nf-core/rnafusion/pull/385)
 - Fix fusion-report issue with MACOXS directories [#386](https://github.com/nf-core/rnafusion/pull/386)
+- The fusion lists is updated to contain two branches, one in case no fusions are detected and one for if fusions are detected, that will be used to feed to fusioninspector, megafusion, arriba visualisation [#388](https://github.com/nf-core/rnafusion/pull/388)
 
 ### Removed
 

subworkflows/local/fusioninspector_workflow.nf

@@ -17,19 +17,23 @@ workflow FUSIONINSPECTOR_WORKFLOW {
     main:
         ch_versions = Channel.empty()
         index ="${params.starfusion_ref}"
-        ch_fusion_list = params.fusioninspector_filter ? fusion_list_filtered : fusion_list
+        ch_fusion_list = ( params.fusioninspector_filter ? fusion_list_filtered : fusion_list )
+        .branch{
+            no_fusions: it[1].size() == 0
+            fusions: it[1].size() > 0
+        }
 
         if (params.whitelist)  {
-            ch_whitelist = ch_fusion_list.combine(Channel.value(file(params.whitelist, checkIfExists:true)))
+            ch_whitelist = ch_fusion_list.fusions.combine(Channel.value(file(params.whitelist, checkIfExists:true)))
                             .map { meta, fusions, whitelist -> [ meta, [fusions, whitelist] ] }
 
             CAT_CAT(ch_whitelist) // fusioninspector takes care of possible duplicates
             ch_versions = ch_versions.mix(CAT_CAT.out.versions)
 
-            ch_fusion_list = CAT_CAT.out.file_out
+            ch_fusion_list.fusions = CAT_CAT.out.file_out
         }
 
-        reads_fusion = reads.join(ch_fusion_list )
+        reads_fusion = reads.join(ch_fusion_list.fusions )
 
         FUSIONINSPECTOR( reads_fusion, index)
         ch_versions = ch_versions.mix(FUSIONINSPECTOR.out.versions)