--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/lib/help/seqkitrmdup.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,61 @@
+// Help text for seqkit rmdup within CPIPES.
+
+def seqkitrmdupHelp(params) {
+
+    Map tool = [:]
+    Map toolspecs = [:]
+    tool.text = [:]
+    tool.helpparams = [:]
+
+    toolspecs = [
+        'seqkit_rmdup_run': [
+            clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' +
+                (params.seqkit_rmdup_run ?: false),
+            cliflag: null,
+            clivalue: null
+        ],
+        'seqkit_rmdup_n': [
+            clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' +
+                "Default: ${params.seqkit_rmdup_n}",
+            cliflag: '-n',
+            clivalue: (params.seqkit_rmdup_n ? ' ' : '')
+        ], 
+        'seqkit_rmdup_s': [
+            clihelp: 'Match and remove duplicate sequences by sequence content. ' +
+                "Default: ${params.seqkit_rmdup_s}",
+            cliflag: '-s',
+            clivalue: (params.seqkit_rmdup_s ? ' ' : '')
+        ],
+        'seqkit_rmdup_d': [
+            clihelp: 'Save the duplicated sequences to a file. ' +
+                "Default: ${params.seqkit_rmdup_d}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'seqkit_rmdup_D': [
+            clihelp: 'Save the number and list of duplicated sequences to a file. ' +
+                "Default: ${params.seqkit_rmdup_D}",
+            cliflag: null,
+            clivalue: null
+        ],
+        'seqkit_rmdup_i': [
+            clihelp: 'Ignore case while using seqkit rmdup. ' +
+                "Default: ${params.seqkit_rmdup_i}",
+            cliflag: '-i',
+            clivalue: (params.seqkit_rmdup_i ? ' ' : '')
+        ],
+        'seqkit_rmdup_P': [
+            clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " +
+                "Default: ${params.seqkit_rmdup_P}",
+            cliflag: '-P',
+            clivalue: (params.seqkit_rmdup_P ? ' ' : '')
+        ]
+    ]
+
+    toolspecs.each {
+        k, v -> tool.text['--' + k] = "${v.clihelp}"
+        tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
+    }
+
+    return tool
+}
\ No newline at end of file