Add dummy channels to circumvent join matching bug

main.nf

@@ -186,12 +186,20 @@ process download_plaza_fasta{
     """
 }
 
+///
+//Due to a Nextflow oddity, the .join() operator only works when at least one match is found
+//Add a dummy match to both channels, which will be filtered out in the next step.
+dummyPlazaChannel = Channel.value(['dummy', 'dummy_cds.fasta', 'dummy_prot.fasta'])
+dummyIncompleteChannel = Channel.value([name: 'dummy'])
+plaza_fasta.mix(dummyPlazaChannel).set{plaza_fasta}
+species_incomplete.mix(dummyIncompleteChannel).set{species_incomplete}
+///
 
 
-    
 species_incomplete
     .map { [ it.name , it ] }
     .join ( plaza_fasta, remainder: true )
+    .filter { it[0] != 'dummy' }
     .map {
 	specie = it[1]
         if (!specie.cds) specie.cds = it[2]