Merge branch 'master' of https://gitlab.psb.ugent.be/deep_genome/pipeline

main.nf

@@ -428,7 +428,7 @@ process of {
 
     output:
     file 'Orthogroups.txt' into orthoGroupsFile
-    set 'clusters*', 'Ortho*', 'Stat*' into ofPublish
+    set 'Orthogroups*', 'Stat*'
 
     script:
     """
@@ -517,13 +517,18 @@ b2gBlastRefSeqInput
     .map {[it.name, it.proteome]}
     .set { b2gBlastRefSeqInput }
 
+//optional parameter to store (big) XML output files
+params.save_b2g_xml = ''
 process b2gBlastRefSeq {
     module 'decypher'
     time null  // no time limit
     cpus 0
     maxForks 1000
     tag "$species"
-    publishDir "${params.output}/blast2go/blasts", mode: 'copy'
+
+    if (params.save_b2g_xml){
+        publishDir "${params.output}/blast2go/blasts", mode: 'copy'
+    }
 
     input:
     set species, file(fasta) from b2gBlastRefSeqInput