--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/lib/help/medakastitch.nf	Thu May 28 20:41:10 2026 +0000
@@ -0,0 +1,49 @@
+// Help text for medaka `stitch` within CPIPES.
+
+def medakastitchHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'medakastitch_min_depth': [
+            clihelp: 'Sites with depth lower than this will not be polished. ' +
+                "Default: ${params.medakastitch_min_depth}",
+            cliflag: '--min_depth',
+            clivalue: (params.medakastitch_min_depth ?: '')
+        ], 
+        'medakastitch_no_fillgaps': [
+            clihelp: "Don't fill gaps in consensus sequence with draft sequence. " +
+                "Default: ${params.medakastitch_no_fillgaps}",
+            cliflag: '--no-fillgaps',
+            clivalue: (params.medakastitch_no_fillgaps ? ' ' : '')
+        ],
+        'medakastitch_fill_char': [
+            clihelp: 'Use a designated character to fill gaps. ' +
+                "Default: ${params.medakastitch_fill_char}",
+            cliflag: '--fill_char',
+            clivalue: (params.medakastitch_fill_char ?: '')
+        ],
+        'medakastitch_regions': [
+            clihelp: 'Genomic regions to analyze, or a bed file. ' +
+                "Default: ${params.medakastitch_regions}",
+            cliflag: '--regions',
+            clivalue: (params.medakastitch_regions ?: '')
+        ],
+        'medakastitch_quals': [
+            clihelp: 'Output with per-base quality scores (fastq). ' +
+                "Default: ${params.medakastitch_quals}",
+            cliflag: '--qualities',
+            clivalue: (params.medakastitch_quals ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file