irma.nf: check that amended_consensus fasta files exist before concat…

…enation using ls instead of compgen
peterk87 · Sep 11, 2023 · 0946f98 · 0946f98
1 parent 2a0d9e7
commit 0946f98
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/local/irma.nf b/modules/local/irma.nf
@@ -37,7 +37,7 @@ process IRMA {
 
  IRMA $irma_module $reads $meta.id
 
- if compgen -G "${meta.id}/amended_consensus/*.fa" > /dev/null; then
+ if ls "${meta.id}/amended_consensus/*.fa" > /dev/null 2>&1; then
  cat ${meta.id}/amended_consensus/*.fa > ${meta.id}.irma.consensus.fasta
  fi
  ln -s .command.log $irma_log