bug fixed in assemble_its (thanks to Kadri Põldmaa for discovering …

…the error)
vmikk · Mar 2, 2023 · df4c8d9 · df4c8d9
1 parent e46cb85
commit df4c8d9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/main.nf b/main.nf
@@ -1175,7 +1175,7 @@ process assemble_its {
  ## Convert table back to fasta
  ## Remove leading and trailing Ns
  echo -e "\n..Preparing fasta"
- awk 'NR>1 { print \$1 "\t" \$2 }' tmp_2_ITS1_58S_ITS2.txt \
+ awk 'NR>1 { print \$1 "\t" \$2\$3\$4 }' tmp_2_ITS1_58S_ITS2.txt \
  | seqkit tab2fx -w 0 \
  | seqkit replace -p "^n+|n+\$" -r "" -is -w 0 \
  | gzip -6 > ${sampID}_ITS1_58S_ITS2.fasta.gz