Add an early check that two paths are provided when providing a comma…

…-separated list.
nf-core · Nov 29, 2023 · 7907df5 · 7907df5
1 parent 56f241b
commit 7907df5
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
@@ -61,7 +61,12 @@ if (params.dada_ref_tax_custom) {
 
 if (params.qiime_ref_tax_custom) {
     if ("${params.qiime_ref_tax_custom}".contains(",")) {
-        ch_qiime_ref_taxonomy = Channel.fromPath(Arrays.asList("${params.qiime_ref_tax_custom}".split(",")), checkIfExists: true)
+        qiime_ref_paths = "${params.qiime_ref_tax_custom}".split(",")
+        if (qiime_ref_paths.length != 2) {
+            error "--qiime_ref_tax_custom accepts a single filepath to a directory or tarball, or two files paths separated by a comma. Please review input."
+        }
+
+        ch_qiime_ref_taxonomy = Channel.fromPath(Arrays.asList(qiime_ref_paths), checkIfExists: true)
     } else {
         ch_qiime_ref_taxonomy = Channel.fromPath("${params.qiime_ref_tax_custom}", checkIfExists: true)
     }