Merge pull request #23 from hoelzer/publish-gff

Publish Prokka GFF and not only the FAA file

Author: hoelzer

main.nf

@@ -106,13 +106,13 @@ include {pocp; pocp_matrix} from './modules/pocp'
 // main workflow
 workflow {
     if (params.genomes) {
-      proteins_ch = prokka(genome_input_ch)
+      proteins_ch = prokka(genome_input_ch).proteins
     } else {
       proteins_ch = proteins_input_ch
     }
 
     // switch to one-vs-all
-    if (params.genome) { protein_ch = prokka_single(genome_single_input_ch) }
+    if (params.genome) { protein_ch = prokka_single(genome_single_input_ch).proteins }
     if (params.protein) { protein_ch = protein_single_input_ch }
 
     if (params.genome || params.protein) {

modules/prokka.nf

@@ -3,12 +3,14 @@
 process prokka {
   label 'prokka'
   publishDir "${params.output}/prokka", mode: 'copy', pattern: "${name}/${name}.faa" 
+  publishDir "${params.output}/prokka", mode: 'copy', pattern: "${name}/${name}.gff" 
 
   input: 
     tuple val(name), path(fasta)
 
   output:
     tuple val(name), path("${name}/${name}.faa"), emit: proteins
+    tuple val(name), path("${name}/${name}.gff"), emit: annotations
 
   script:
     """