From fa05f11ed69eb19c35dd7bbbba373ce6d2b2b03b Mon Sep 17 00:00:00 2001
From: DOH-JDJ0303 <jared.johnson@doh.wa.gov>
Date: Sat, 27 Apr 2024 10:11:53 -0700
Subject: [PATCH] val to path

---
 modules/local/assign-remainder.nf |  2 +-
 nextflow_schema.json              | 24 ++++++++++--------------
 2 files changed, 11 insertions(+), 15 deletions(-)

diff --git a/modules/local/assign-remainder.nf b/modules/local/assign-remainder.nf
index 4d991ae..ea84244 100644
--- a/modules/local/assign-remainder.nf
+++ b/modules/local/assign-remainder.nf
@@ -5,7 +5,7 @@ process ASSIGN_REMAINDER {
     stageInMode 'copy'
 
     input:
-    tuple val(taxa), val(segment), path(reps), val(mash), val(all)
+    tuple val(taxa), val(segment), path(reps), path(mash), path(all)
 
     output:
     tuple val(taxa), val(segment), path("${prefix}-assigned.csv"), emit: assigned
diff --git a/nextflow_schema.json b/nextflow_schema.json
index daf22ae..992076a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,10 +10,7 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": [
-                "input",
-                "outdir"
-            ],
+            "required": ["input", "outdir"],
             "properties": {
                 "input": {
                     "type": "string",
@@ -201,14 +198,7 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": [
-                        "symlink",
-                        "rellink",
-                        "link",
-                        "copy",
-                        "copyNoFollow",
-                        "move"
-                    ],
+                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -314,5 +304,11 @@
         {
             "$ref": "#/definitions/generic_options"
         }
-    ]
-}
\ No newline at end of file
+    ],
+    "properties": {
+        "max_cluster": {
+            "type": "integer",
+            "default": 10000
+        }
+    }
+}