From f4207022dcb13934bb1fd9f13fec222e82310781 Mon Sep 17 00:00:00 2001
From: Greg <harper357@gmail.com>
Date: Thu, 24 Apr 2025 14:25:45 -0700
Subject: [PATCH 1/2] update cobra params

---
 nextflow_schema.json | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index dc4a29b..6f5b931 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -152,14 +152,15 @@
                 },
                 "cobra_assembler": {
                     "type": "string",
-                    "description": "The assembler that was used to assemble viral contigs"
+                    "description": "The assembler that was used to assemble viral contigs",
+                    "enum": ["idba", "metaspades", "megahit"]
                 },
                 "cobra_mink": {
-                    "type": "string",
+                    "type": "integer",
                     "description": "Minimum kmer value used during assembly"
                 },
                 "cobra_maxk": {
-                    "type": "string",
+                    "type": "integer",
                     "description": "Maximum kmer value used during assembly"
                 }
             }

From 70df1641ad94ff48f1c7ecd1c82c3de4585be398 Mon Sep 17 00:00:00 2001
From: Greg <harper357@gmail.com>
Date: Thu, 24 Apr 2025 14:32:42 -0700
Subject: [PATCH 2/2] added test config

---
 conf/test_cobra.config | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 conf/test_cobra.config

diff --git a/conf/test_cobra.config b/conf/test_cobra.config
new file mode 100644
index 0000000..e7afd88
--- /dev/null
+++ b/conf/test_cobra.config
@@ -0,0 +1,33 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/phageannotator -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Test COBRA profile'
+    config_profile_description = 'Minimal test dataset to check COBRA function '
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus   = 2
+    max_memory = '6.GB'
+    max_time   = '6.h'
+
+    // Input data
+    input  = 'https://github.com/nf-core/test-datasets/raw/phageannotator/assets/1.0.0/test_samplesheet.csv'
+
+    // Tool options
+    run_cobra                       = true
+    cobra_assembler                 = 'megahit'
+    cobra_mink                      = 21
+    cobra_maxk                      = 141
+
+    // Pipeline options
+    publish_dir_mode                = 'symlink'
+}