fix typo in nextflow config related to fna_faa_gff

bactopia · Apr 8, 2024 · cfd4c12 · cfd4c12
1 parent f0f3b32
commit cfd4c12
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/lib/nf/bactopia_tools.nf b/lib/nf/bactopia_tools.nf
@@ -177,12 +177,12 @@ def _collect_inputs(sample, dir, extension) {
         if (!file("${faa}").exists() && !file("${faa}.gz").exists()) {
             // Fall back on Prokka
             faa = "${base_dir}/${PATHS['faa']}/prokka/${sample}.faa"
-            gff = "${base_dir}/${PATHS['faa']}/bakta/${sample}.gff"
+            gff = "${base_dir}/${PATHS['faa']}/prokka/${sample}.gff"
         }
 
         if (file("${fna}.gz").exists() && file("${faa}.gz").exists() && file("${gff}.gz").exists()) {
             return tuple([id:sample, is_compressed:true], [file("${fna}.gz")], [file("${faa}.gz")], [file("${gff}.gz")])
-        } else if (file(fna).exists() && file(faa).exists() && file(gff).exists() {
+        } else if (file(fna).exists() && file(faa).exists() && file(gff).exists()) {
             return tuple([id:sample, is_compressed:false], [file("${fna}")], [file("${faa}")], [file("${gff}")])
         }
     } else if (extension == 'fna_faa') {