Add --organism arg to amrfinderplus

genomic-medicine-sweden · Feb 16, 2024 · ce5ea29 · ce5ea29
1 parent c4a31c9
commit ce5ea29
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/nextflow-modules/modules/amrfinderplus/main.nf b/nextflow-modules/modules/amrfinderplus/main.nf
@@ -30,6 +30,7 @@ process amrfinderplus {
     --nucleotide $assembly \\
     $database_command \\
     $args \\
+    --organism $taxonName \\
     --output $output
 
     cat <<-END_VERSIONS > ${sampleName}_${task.process}_versions.yml