From cd0b46c50714170199ba487b1ca9be3e0e09de9b Mon Sep 17 00:00:00 2001
From: Adam Bennett <adbennett@minderoo.org>
Date: Fri, 12 Apr 2024 09:30:31 +0800
Subject: [PATCH 1/2] added pattern to ncbidownload_group's input validation to
 allow a comma separated list of groups

---
 nextflow_schema.json | 14 +-------------
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 03f9fa8..b49f205 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -372,19 +372,7 @@
                     "type": "string",
                     "default": "all",
                     "description": "The NCBI taxonomic groups to download. Options include 'all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', and 'viral'. A comma-separated list is also valid (e.g., 'bacteria,viral').",
-                    "enum": [
-                        "all",
-                        "archaea",
-                        "bacteria",
-                        "fungi",
-                        "invertebrate",
-                        "metagenomes",
-                        "plant",
-                        "protozoa",
-                        "vertebrate_mammalian",
-                        "vertebrate_other",
-                        "viral"
-                    ]
+                    "pattern": "^(?:[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+(?:,[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+)*)?$"
                 },
                 "ncbidownload_section": {
                     "type": "string",

From 288be93223eb02a77249821ffff9d79b2e18bf7d Mon Sep 17 00:00:00 2001
From: Adam Bennett <43841526+a4000@users.noreply.github.com>
Date: Mon, 15 Apr 2024 13:46:57 +0800
Subject: [PATCH 2/2] Update nextflow_schema.json
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index b49f205..2db9bd0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -372,7 +372,7 @@
                     "type": "string",
                     "default": "all",
                     "description": "The NCBI taxonomic groups to download. Options include 'all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', and 'viral'. A comma-separated list is also valid (e.g., 'bacteria,viral').",
-                    "pattern": "^(?:[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+(?:,[all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral]+)*)?$"
+                    "pattern": "^((all|archaea|bacteria|fungi|invertebrate|metagenomes|plant|protozoa|vertebrate_mammalian|vertebrate_other|viral)?,?)*(?<!,)$"
                 },
                 "ncbidownload_section": {
                     "type": "string",