From 7907df5bfb4843a80352e8de18265c7331c4ba8a Mon Sep 17 00:00:00 2001
From: Matthew Marshall <matthew.marshall@stfc.ac.uk>
Date: Wed, 29 Nov 2023 15:49:02 -0500
Subject: [PATCH] Add an early check that two paths are provided when providing
 a comma-separated list.

---
 workflows/ampliseq.nf | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/workflows/ampliseq.nf b/workflows/ampliseq.nf
index 3a332326..a99e71f9 100644
--- 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)
     }