From cf6cac8682efb082c47f6096fea3115a0ce91674 Mon Sep 17 00:00:00 2001
From: Mohammed Mahdi <mohammed.mahdi@oist.jp>
Date: Wed, 17 Apr 2024 17:08:05 +0900
Subject: [PATCH] Added a 'target' parameter

---
 nextflow.config      |  3 ++-
 nextflow_schema.json | 22 ++++++++++++++++++++--
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 74224dc..76688b3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,8 +10,9 @@
 params {
 
     // TODO nf-core: Specify your pipeline's command line flags
-    // Input options
+    // Mandatory options
     input                      = null
+    target                     = null
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7eae368..b381e70 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,7 +10,11 @@
             "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",
+                "target"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -23,6 +27,13 @@
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/pairalign/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
                 },
+                "target": {
+                    "type": "string",
+                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
+                    "format": "file-path",
+                    "description": "Path to FASTA genome file for the target genome.",
+                    "fa_icon": "far fa-file-code"
+                },
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",
@@ -182,7 +193,14 @@
                     "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": {