From ff1f28f4f0b8e88898e0f568f83e2da90ff81bc6 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 25 Mar 2022 15:01:25 +0100
Subject: [PATCH] Update schema

---
 conf/modules.config  |  4 ++--
 nextflow_schema.json | 38 +++++++++++++++++++++++++++++++++++---
 2 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 36bc626..1052bed 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -69,8 +69,8 @@ process {
             params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
             // trimming options
             params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
-            params.shortread_adapter1 ? "--adapter_sequence ${params.shortread_adapter1}" : "",
-            !{ ${meta.single_end} } && params.shortread_adapter2 ? "--adapter_sequence_r2 ${params.shortread_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : ""
+            params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
+            !{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
             // filtering options
             "--length_required ${params.shortread_clipmerge_minlength}"
         ].join(' ').trim()
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0fa217f..42307e9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -10,7 +10,10 @@
             "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",
@@ -173,7 +176,14 @@
                     "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": {
@@ -281,6 +291,28 @@
         },
         "run_kraken2": {
             "type": "boolean"
+        },
+        "shortread_clipmerge_tool": {
+            "type": "string",
+            "default": "fastp"
+        },
+        "shortread_clipmerge_skiptrim": {
+            "type": "boolean"
+        },
+        "shortread_clipmerge_mergepairs": {
+            "type": "boolean"
+        },
+        "shortread_clipmerge_adapter1": {
+            "type": "string",
+            "default": null
+        },
+        "shortread_clipmerge_adapter2": {
+            "type": "string",
+            "default": null
+        },
+        "shortread_clipmerge_minlength": {
+            "type": "integer",
+            "default": 15
         }
     }
-}
+}
\ No newline at end of file