Merge pull request nf-core#33 from itrujnara/bug_fixes

Fixed local OMA bug
JoseEspinosa · May 27, 2024 · f29a393 · f29a393
2 parents f85f4f5 + 3dfb5c4
commit f29a393
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/modules/local/fetch_oma_group_local.nf b/modules/local/fetch_oma_group_local.nf
@@ -30,7 +30,7 @@ process FETCH_OMA_GROUP_LOCAL {
     prefix = task.ext.prefix ?: meta.id
     """
     omaid=\$(uniprot2oma_local.py $uniprot_idmap $uniprot_id)
-    zcat $db | grep \$omaid | head -1 | cut -f3- > ${prefix}_oma_group_oma.txt || test -f ${prefix}_oma_group_oma.txt
+    zcat $db | grep \$omaid | head -1 | cut -f3- | awk '{gsub(/\\t/,"\\n"); print}' > ${prefix}_oma_group_oma.txt || test -f ${prefix}_oma_group_oma.txt
     oma2uniprot_local.py $uniprot_idmap ${prefix}_oma_group_oma.txt > ${prefix}_oma_group_raw.txt
     uniprotize_oma_local.py ${prefix}_oma_group_raw.txt $ensembl_idmap $refseq_idmap > ${prefix}_oma_group.txt
     csv_adorn.py ${prefix}_oma_group.txt OMA > ${prefix}_oma_group.csv