Check gff validity (issue : check point prokka)

modules/prokka.nf

@@ -7,11 +7,18 @@ process PROKKA {
    output:
    tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results
    path "PROKKA_${sampleId}/${sampleId}.txt", emit: report
+   path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results
 
   script:
   """
   prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus}
   rm PROKKA_${sampleId}/*.gbk
+
+  gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
+  if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt
+  then
+    rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt 
+  fi
   """
 }